From 6a6d28a4245802b0b8bdef33dabbeecb04ec8ff3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 30 Jun 2022 13:25:22 +0200 Subject: [PATCH] Revert "fix: give conda-forge highest priority to ensure proper semantic under strict channel priorities" This reverts commit ce78f79fb3fd5740e414b93f9f62cee72f7dcf38. --- bio/adapterremoval/environment.yaml | 1 + bio/arriba/environment.yaml | 1 + bio/art/profiler_illumina/environment.yaml | 2 +- bio/assembly-stats/environment.yaml | 2 +- bio/bamtools/filter/environment.yaml | 2 +- bio/bamtools/filter_json/environment.yaml | 2 +- bio/bamtools/split/environment.yaml | 2 +- bio/bamtools/stats/environment.yaml | 2 +- bio/bbtools/bbduk/environment.yaml | 3 ++- bio/bcftools/call/environment.yaml | 2 +- bio/bcftools/concat/environment.yaml | 2 +- bio/bcftools/filter/environment.yaml | 3 ++- bio/bcftools/index/environment.yaml | 2 +- bio/bcftools/merge/environment.yaml | 2 +- bio/bcftools/mpileup/environment.yaml | 2 +- bio/bcftools/norm/environment.yaml | 2 +- bio/bcftools/reheader/environment.yaml | 2 +- bio/bcftools/sort/environment.yaml | 2 +- bio/bcftools/stats/environment.yaml | 2 +- bio/bcftools/view/environment.yaml | 2 +- bio/bedtools/complement/environment.yaml | 3 ++- bio/bedtools/coveragebed/environment.yaml | 3 ++- bio/bedtools/genomecov/environment.yaml | 3 ++- bio/bedtools/intersect/environment.yaml | 3 ++- bio/bedtools/merge/environment.yaml | 3 ++- bio/bedtools/slop/environment.yaml | 3 ++- bio/bedtools/sort/environment.yaml | 3 ++- bio/benchmark/chm-eval-sample/environment.yaml | 2 +- bio/bgzip/environment.yaml | 2 +- bio/biobambam2/bamsormadup/environment.yaml | 3 ++- bio/bismark/bam2nuc/environment.yaml | 3 ++- bio/bismark/bismark/environment.yaml | 3 ++- bio/bismark/bismark2bedGraph/environment.yaml | 3 ++- bio/bismark/bismark2report/environment.yaml | 3 ++- bio/bismark/bismark2summary/environment.yaml | 3 ++- bio/bismark/bismark_genome_preparation/environment.yaml | 3 ++- bio/bismark/bismark_methylation_extractor/environment.yaml | 3 ++- bio/bismark/deduplicate_bismark/environment.yaml | 3 ++- bio/blast/blastn/environment.yaml | 3 ++- bio/blast/makeblastdb/environment.yaml | 3 ++- bio/bowtie2/align/environment.yaml | 3 ++- bio/bowtie2/build/environment.yaml | 3 ++- bio/busco/environment.yaml | 3 ++- bio/bwa-mem2/index/environment.yaml | 3 ++- bio/bwa-mem2/mem-samblaster/environment.yaml | 3 ++- bio/bwa-mem2/mem/environment.yaml | 3 ++- bio/bwa/aln/environment.yaml | 3 ++- bio/bwa/index/environment.yaml | 3 ++- bio/bwa/mem-samblaster/environment.yaml | 3 ++- bio/bwa/mem/environment.yaml | 3 ++- bio/bwa/sampe/environment.yaml | 2 +- bio/bwa/samse/environment.yaml | 2 +- bio/bwa/samxe/environment.yaml | 2 +- bio/clustalo/environment.yaml | 2 +- bio/cutadapt/pe/environment.yaml | 3 ++- bio/cutadapt/se/environment.yaml | 3 ++- bio/dada2/add-species/environment.yaml | 3 ++- bio/dada2/assign-species/environment.yaml | 3 ++- bio/dada2/assign-taxonomy/environment.yaml | 3 ++- bio/dada2/collapse-nomismatch/environment.yaml | 3 ++- bio/dada2/dereplicate-fastq/environment.yaml | 3 ++- bio/dada2/filter-trim/environment.yaml | 3 ++- bio/dada2/learn-errors/environment.yaml | 3 ++- bio/dada2/make-table/environment.yaml | 3 ++- bio/dada2/merge-pairs/environment.yaml | 3 ++- bio/dada2/quality-profile/environment.yaml | 3 ++- bio/dada2/remove-chimeras/environment.yaml | 3 ++- bio/dada2/sample-inference/environment.yaml | 3 ++- bio/deeptools/computematrix/environment.yaml | 1 + bio/deeptools/plotfingerprint/environment.yaml | 1 + bio/deeptools/plotheatmap/environment.yaml | 1 + bio/deeptools/plotprofile/environment.yaml | 1 + bio/delly/environment.yaml | 2 +- bio/diamond/blastp/environment.yaml | 2 +- bio/diamond/blastx/environment.yaml | 3 ++- bio/diamond/makedb/environment.yaml | 3 ++- bio/dragmap/align/environment.yaml | 3 ++- bio/dragmap/build/environment.yaml | 3 ++- bio/epic/peaks/environment.yaml | 3 ++- bio/fastp/environment.yaml | 3 ++- bio/fastq_screen/environment.yaml | 3 ++- bio/fastqc/environment.yaml | 3 ++- bio/fasttree/environment.yaml | 2 +- bio/fgbio/annotatebamwithumis/environment.yaml | 3 ++- bio/fgbio/callmolecularconsensusreads/environment.yaml | 3 ++- bio/fgbio/collectduplexseqmetrics/environment.yaml | 3 ++- bio/fgbio/filterconsensusreads/environment.yaml | 3 ++- bio/fgbio/groupreadsbyumi/environment.yaml | 3 ++- bio/fgbio/setmateinformation/environment.yaml | 3 ++- bio/freebayes/environment.yaml | 2 +- bio/gatk/applybqsr/environment.yaml | 3 ++- bio/gatk/applybqsrspark/environment.yaml | 3 ++- bio/gatk/applyvqsr/environment.yaml | 3 ++- bio/gatk/baserecalibrator/environment.yaml | 3 ++- bio/gatk/baserecalibratorspark/environment.yaml | 3 ++- bio/gatk/cleansam/environment.yaml | 3 ++- bio/gatk/combinegvcfs/environment.yaml | 3 ++- bio/gatk/estimatelibrarycomplexity/environment.yaml | 3 ++- bio/gatk/filtermutectcalls/environment.yaml | 3 ++- bio/gatk/genomicsdbimport/environment.yaml | 3 ++- bio/gatk/genotypegvcfs/environment.yaml | 3 ++- bio/gatk/haplotypecaller/environment.yaml | 3 ++- bio/gatk/intervallisttobed/environment.yaml | 3 ++- bio/gatk/markduplicatesspark/environment.yaml | 3 ++- bio/gatk/mutect/environment.yaml | 3 ++- bio/gatk/printreadsspark/environment.yaml | 3 ++- bio/gatk/scatterintervalsbyns/environment.yaml | 3 ++- bio/gatk/selectvariants/environment.yaml | 3 ++- bio/gatk/splitncigarreads/environment.yaml | 3 ++- bio/gatk/variantannotator/environment.yaml | 3 ++- bio/gatk/varianteval/environment.yaml | 3 ++- bio/gatk/variantfiltration/environment.yaml | 3 ++- bio/gatk/variantrecalibrator/environment.yaml | 3 ++- bio/gatk3/baserecalibrator/environment.yaml | 3 ++- bio/gatk3/indelrealigner/environment.yaml | 3 ++- bio/gatk3/printreads/environment.yaml | 3 ++- bio/gatk3/realignertargetcreator/environment.yaml | 3 ++- bio/gdc-client/download/environment.yaml | 2 +- bio/genomepy/environment.yaml | 1 + bio/gridss/assemble/environment.yaml | 3 ++- bio/gridss/call/environment.yaml | 3 ++- bio/gridss/preprocess/environment.yaml | 3 ++- bio/gridss/setupreference/environment.yaml | 3 ++- bio/hap.py/hap.py/environment.yaml | 3 ++- bio/hap.py/pre.py/environment.yaml | 3 ++- bio/hisat2/align/environment.yaml | 1 + bio/hisat2/index/environment.yaml | 1 + bio/hmmer/hmmbuild/environment.yaml | 1 + bio/hmmer/hmmpress/environment.yaml | 1 + bio/hmmer/hmmscan/environment.yaml | 1 + bio/hmmer/hmmsearch/environment.yaml | 1 + bio/homer/annotatePeaks/environment.yaml | 2 +- bio/homer/findPeaks/environment.yaml | 2 +- bio/homer/getDifferentialPeaks/environment.yaml | 2 +- bio/homer/makeTagDirectory/environment.yaml | 2 +- bio/homer/mergePeaks/environment.yaml | 2 +- bio/infernal/cmpress/environment.yaml | 3 ++- bio/infernal/cmscan/environment.yaml | 3 ++- bio/jannovar/environment.yaml | 3 ++- bio/jellyfish/count/environment.yaml | 3 ++- bio/jellyfish/dump/environment.yaml | 3 ++- bio/jellyfish/histo/environment.yaml | 3 ++- bio/jellyfish/merge/environment.yaml | 3 ++- bio/kallisto/index/environment.yaml | 3 ++- bio/kallisto/quant/environment.yaml | 3 ++- bio/last/lastal/environment.yaml | 3 ++- bio/last/lastdb/environment.yaml | 3 ++- bio/liftoff/environment.yaml | 2 +- bio/lofreq/call/environment.yaml | 2 +- bio/macs2/callpeak/environment.yaml | 1 + bio/manta/environment.yaml | 3 ++- bio/mapdamage2/environment.yaml | 3 ++- bio/mashmap/environment.yaml | 3 ++- bio/microphaser/build_reference/environment.yaml | 2 +- bio/microphaser/filter/environment.yaml | 2 +- bio/microphaser/normal/environment.yaml | 2 +- bio/microphaser/somatic/environment.yaml | 2 +- bio/minimap2/aligner/environment.yaml | 3 ++- bio/minimap2/index/environment.yaml | 3 ++- bio/mlst/environment.yaml | 2 +- bio/mosdepth/environment.yaml | 3 ++- bio/msisensor/msi/environment.yaml | 3 ++- bio/msisensor/scan/environment.yaml | 3 ++- bio/multiqc/environment.yaml | 3 ++- bio/muscle/environment.yaml | 2 +- bio/nanosim-h/environment.yaml | 2 +- bio/ngs-disambiguate/environment.yaml | 3 ++- bio/optitype/environment.yaml | 1 + bio/paladin/align/environment.yaml | 3 ++- bio/paladin/index/environment.yaml | 3 ++- bio/paladin/prepare/environment.yaml | 3 ++- bio/pandora/index/environment.yaml | 2 +- bio/pbmm2/align/environment.yaml | 3 ++- bio/pbmm2/index/environment.yaml | 3 ++- bio/pear/environment.yaml | 3 ++- bio/picard/addorreplacereadgroups/environment.yaml | 3 ++- bio/picard/bedtointervallist/environment.yaml | 3 ++- bio/picard/collectalignmentsummarymetrics/environment.yaml | 3 ++- bio/picard/collectgcbiasmetrics/environment.yaml | 3 ++- bio/picard/collecthsmetrics/environment.yaml | 3 ++- bio/picard/collectinsertsizemetrics/environment.yaml | 3 ++- bio/picard/collectmultiplemetrics/environment.yaml | 3 ++- bio/picard/collectrnaseqmetrics/environment.yaml | 3 ++- bio/picard/collecttargetedpcrmetrics/environment.yaml | 3 ++- bio/picard/createsequencedictionary/environment.yaml | 3 ++- bio/picard/markduplicates/environment.yaml | 3 ++- bio/picard/markduplicateswithmatecigar/environment.yaml | 3 ++- bio/picard/mergesamfiles/environment.yaml | 3 ++- bio/picard/mergevcfs/environment.yaml | 3 ++- bio/picard/revertsam/environment.yaml | 3 ++- bio/picard/samtofastq/environment.yaml | 3 ++- bio/picard/sortsam/environment.yaml | 3 ++- bio/pindel/call/environment.yaml | 3 ++- bio/pindel/pindel2vcf/environment.yaml | 3 ++- bio/plass/environment.yaml | 3 ++- bio/prosolo/control-fdr/environment.yaml | 3 ++- bio/prosolo/single-cell-bulk/environment.yaml | 3 ++- bio/ptrimmer/environment.yaml | 2 +- bio/qualimap/rnaseq/environment.yaml | 3 ++- bio/rasusa/environment.yaml | 2 +- bio/razers3/environment.yaml | 1 + bio/rbt/csvreport/environment.yaml | 2 +- bio/rebaler/environment.yaml | 3 ++- bio/reference/ensembl-variation/environment.yaml | 2 +- bio/refgenie/environment.yaml | 2 +- bio/salmon/decoys/environment.yaml | 1 + bio/salmon/index/environment.yaml | 3 ++- bio/salmon/quant/environment.yaml | 3 ++- bio/sambamba/flagstat/environment.yaml | 3 ++- bio/sambamba/index/environment.yaml | 3 ++- bio/sambamba/markdup/environment.yaml | 3 ++- bio/sambamba/merge/environment.yaml | 3 ++- bio/sambamba/slice/environment.yaml | 3 ++- bio/sambamba/sort/environment.yaml | 3 ++- bio/sambamba/view/environment.yaml | 3 ++- bio/samtools/calmd/environment.yaml | 2 +- bio/samtools/depth/environment.yaml | 2 +- bio/samtools/faidx/environment.yaml | 2 +- bio/samtools/fastx/environment.yaml | 3 ++- bio/samtools/fixmate/environment.yaml | 3 ++- bio/samtools/flagstat/environment.yaml | 2 +- bio/samtools/idxstats/environment.yaml | 2 +- bio/samtools/index/environment.yaml | 2 +- bio/samtools/merge/environment.yaml | 2 +- bio/samtools/mpileup/environment.yaml | 2 +- bio/samtools/sort/environment.yaml | 2 +- bio/samtools/stats/environment.yaml | 2 +- bio/samtools/view/environment.yaml | 2 +- bio/seqtk/mergepe/environment.yaml | 2 +- bio/seqtk/seq/environment.yaml | 2 +- bio/seqtk/subsample/pe/environment.yaml | 2 +- bio/seqtk/subsample/se/environment.yaml | 2 +- bio/shovill/environment.yaml | 3 ++- bio/sickle/pe/environment.yaml | 3 ++- bio/sickle/se/environment.yaml | 3 ++- bio/snp-mutator/environment.yaml | 2 +- bio/snpeff/annotate/environment.yaml | 2 +- bio/snpeff/download/environment.yaml | 2 +- bio/snpsift/annotate/environment.yaml | 2 +- bio/snpsift/dbnsfp/environment.yaml | 2 +- bio/snpsift/genesets/environment.yaml | 2 +- bio/snpsift/gwascat/environment.yaml | 2 +- bio/snpsift/varType/environment.yaml | 2 +- bio/sourmash/compute/environment.yaml | 3 ++- bio/spades/metaspades/environment.yaml | 3 ++- bio/sra-tools/fasterq-dump/environment.yaml | 2 +- bio/star/align/environment.yaml | 2 +- bio/star/index/environment.yaml | 2 +- bio/strelka/germline/environment.yaml | 3 ++- bio/strelka/somatic/environment.yaml | 3 ++- bio/strling/call/environment.yaml | 3 ++- bio/strling/extract/environment.yaml | 3 ++- bio/strling/index/environment.yaml | 3 ++- bio/strling/merge/environment.yaml | 3 ++- bio/subread/featurecounts/environment.yaml | 3 ++- bio/tabix/environment.yaml | 2 +- bio/tabix/query/environment.yaml | 2 +- bio/transdecoder/longorfs/environment.yaml | 3 ++- bio/transdecoder/predict/environment.yaml | 3 ++- bio/trim_galore/pe/environment.yaml | 3 ++- bio/trim_galore/se/environment.yaml | 3 ++- bio/trimmomatic/pe/environment.yaml | 3 ++- bio/trimmomatic/se/environment.yaml | 3 ++- bio/trinity/environment.yaml | 3 ++- bio/tximport/environment.yaml | 3 ++- bio/ucsc/bedGraphToBigWig/environment.yaml | 3 ++- bio/ucsc/faToTwoBit/environment.yaml | 3 ++- bio/ucsc/gtfToGenePred/environment.yaml | 3 ++- bio/ucsc/twoBitInfo/environment.yaml | 3 ++- bio/ucsc/twoBitToFa/environment.yaml | 3 ++- bio/umis/bamtag/environment.yaml | 2 +- bio/unicycler/environment.yaml | 2 +- bio/varscan/mpileup2indel/environment.yaml | 3 ++- bio/varscan/mpileup2snp/environment.yaml | 3 ++- bio/varscan/somatic/environment.yaml | 3 ++- bio/vcftools/filter/environment.yaml | 3 ++- bio/vembrane/filter/environment.yaml | 2 +- bio/vembrane/table/environment.yaml | 2 +- bio/vep/annotate/environment.yaml | 2 +- bio/vep/cache/environment.yaml | 2 +- bio/vg/construct/environment.yaml | 2 +- bio/vg/ids/environment.yaml | 2 +- bio/vg/index/gcsa/environment.yaml | 2 +- bio/vg/index/xg/environment.yaml | 2 +- bio/vg/kmers/environment.yaml | 2 +- bio/vg/merge/environment.yaml | 2 +- bio/vg/prune/environment.yaml | 2 +- bio/vg/sim/environment.yaml | 2 +- bio/wgsim/environment.yaml | 2 +- utils/cairosvg/environment.yaml | 2 +- utils/nextflow/environment.yaml | 2 +- 291 files changed, 473 insertions(+), 274 deletions(-) diff --git a/bio/adapterremoval/environment.yaml b/bio/adapterremoval/environment.yaml index 912f10652b..9991543160 100644 --- a/bio/adapterremoval/environment.yaml +++ b/bio/adapterremoval/environment.yaml @@ -1,4 +1,5 @@ channels: - bioconda + - defaults dependencies: - adapterremoval =2.3 diff --git a/bio/arriba/environment.yaml b/bio/arriba/environment.yaml index a9a15d5dfd..46e780285b 100644 --- a/bio/arriba/environment.yaml +++ b/bio/arriba/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - arriba ==1.1.0 diff --git a/bio/art/profiler_illumina/environment.yaml b/bio/art/profiler_illumina/environment.yaml index 51d4e272d9..5d9cc745dd 100644 --- a/bio/art/profiler_illumina/environment.yaml +++ b/bio/art/profiler_illumina/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - art ==2016.06.05 diff --git a/bio/assembly-stats/environment.yaml b/bio/assembly-stats/environment.yaml index 7b70f02daa..56381cb73c 100644 --- a/bio/assembly-stats/environment.yaml +++ b/bio/assembly-stats/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - assembly-stats=1.0 diff --git a/bio/bamtools/filter/environment.yaml b/bio/bamtools/filter/environment.yaml index b9cf58206f..5015d57e84 100644 --- a/bio/bamtools/filter/environment.yaml +++ b/bio/bamtools/filter/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bamtools ==2.5.1 diff --git a/bio/bamtools/filter_json/environment.yaml b/bio/bamtools/filter_json/environment.yaml index b9cf58206f..5015d57e84 100644 --- a/bio/bamtools/filter_json/environment.yaml +++ b/bio/bamtools/filter_json/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bamtools ==2.5.1 diff --git a/bio/bamtools/split/environment.yaml b/bio/bamtools/split/environment.yaml index b9cf58206f..5015d57e84 100644 --- a/bio/bamtools/split/environment.yaml +++ b/bio/bamtools/split/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bamtools ==2.5.1 diff --git a/bio/bamtools/stats/environment.yaml b/bio/bamtools/stats/environment.yaml index b9cf58206f..5015d57e84 100644 --- a/bio/bamtools/stats/environment.yaml +++ b/bio/bamtools/stats/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bamtools ==2.5.1 diff --git a/bio/bbtools/bbduk/environment.yaml b/bio/bbtools/bbduk/environment.yaml index 5e682d7f24..c1bb92cce2 100644 --- a/bio/bbtools/bbduk/environment.yaml +++ b/bio/bbtools/bbduk/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bbmap ==38.90 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/bcftools/call/environment.yaml b/bio/bcftools/call/environment.yaml index cb64c0963a..9c56d28611 100644 --- a/bio/bcftools/call/environment.yaml +++ b/bio/bcftools/call/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 \ No newline at end of file diff --git a/bio/bcftools/concat/environment.yaml b/bio/bcftools/concat/environment.yaml index 7ae350767e..45e14167f3 100644 --- a/bio/bcftools/concat/environment.yaml +++ b/bio/bcftools/concat/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.12 - snakemake-wrapper-utils ==0.2.0 diff --git a/bio/bcftools/filter/environment.yaml b/bio/bcftools/filter/environment.yaml index 5a2a03e8e8..5dfd8a1d14 100644 --- a/bio/bcftools/filter/environment.yaml +++ b/bio/bcftools/filter/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bcftools ==1.12 - snakemake-wrapper-utils ==0.2 diff --git a/bio/bcftools/index/environment.yaml b/bio/bcftools/index/environment.yaml index cb64c0963a..9c56d28611 100644 --- a/bio/bcftools/index/environment.yaml +++ b/bio/bcftools/index/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 \ No newline at end of file diff --git a/bio/bcftools/merge/environment.yaml b/bio/bcftools/merge/environment.yaml index cb64c0963a..9c56d28611 100644 --- a/bio/bcftools/merge/environment.yaml +++ b/bio/bcftools/merge/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 \ No newline at end of file diff --git a/bio/bcftools/mpileup/environment.yaml b/bio/bcftools/mpileup/environment.yaml index cb64c0963a..9c56d28611 100644 --- a/bio/bcftools/mpileup/environment.yaml +++ b/bio/bcftools/mpileup/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 \ No newline at end of file diff --git a/bio/bcftools/norm/environment.yaml b/bio/bcftools/norm/environment.yaml index 485b4e5a18..2087690b5f 100644 --- a/bio/bcftools/norm/environment.yaml +++ b/bio/bcftools/norm/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 - snakemake-wrapper-utils =0.2 diff --git a/bio/bcftools/reheader/environment.yaml b/bio/bcftools/reheader/environment.yaml index cb64c0963a..9c56d28611 100644 --- a/bio/bcftools/reheader/environment.yaml +++ b/bio/bcftools/reheader/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 \ No newline at end of file diff --git a/bio/bcftools/sort/environment.yaml b/bio/bcftools/sort/environment.yaml index cd2b770bab..6d9e0c8b98 100644 --- a/bio/bcftools/sort/environment.yaml +++ b/bio/bcftools/sort/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools ==1.11 diff --git a/bio/bcftools/stats/environment.yaml b/bio/bcftools/stats/environment.yaml index 3aaa56355d..4cfa378a2c 100644 --- a/bio/bcftools/stats/environment.yaml +++ b/bio/bcftools/stats/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools ==1.12 diff --git a/bio/bcftools/view/environment.yaml b/bio/bcftools/view/environment.yaml index 5a2a03e8e8..b0659bb80c 100644 --- a/bio/bcftools/view/environment.yaml +++ b/bio/bcftools/view/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools ==1.12 - snakemake-wrapper-utils ==0.2 diff --git a/bio/bedtools/complement/environment.yaml b/bio/bedtools/complement/environment.yaml index cdadf069f7..e66eced385 100644 --- a/bio/bedtools/complement/environment.yaml +++ b/bio/bedtools/complement/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools =2.29 diff --git a/bio/bedtools/coveragebed/environment.yaml b/bio/bedtools/coveragebed/environment.yaml index f1614bdcbe..4e358ae4b3 100644 --- a/bio/bedtools/coveragebed/environment.yaml +++ b/bio/bedtools/coveragebed/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools ==2.29.0 diff --git a/bio/bedtools/genomecov/environment.yaml b/bio/bedtools/genomecov/environment.yaml index 58f5fa3827..5bceea5ebe 100644 --- a/bio/bedtools/genomecov/environment.yaml +++ b/bio/bedtools/genomecov/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools ==2.29.2 diff --git a/bio/bedtools/intersect/environment.yaml b/bio/bedtools/intersect/environment.yaml index 0f7dafdadc..fdd252c16f 100644 --- a/bio/bedtools/intersect/environment.yaml +++ b/bio/bedtools/intersect/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools =2.29.0 diff --git a/bio/bedtools/merge/environment.yaml b/bio/bedtools/merge/environment.yaml index 0f7dafdadc..fdd252c16f 100644 --- a/bio/bedtools/merge/environment.yaml +++ b/bio/bedtools/merge/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools =2.29.0 diff --git a/bio/bedtools/slop/environment.yaml b/bio/bedtools/slop/environment.yaml index 0f7dafdadc..fdd252c16f 100644 --- a/bio/bedtools/slop/environment.yaml +++ b/bio/bedtools/slop/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools =2.29.0 diff --git a/bio/bedtools/sort/environment.yaml b/bio/bedtools/sort/environment.yaml index cdadf069f7..e66eced385 100644 --- a/bio/bedtools/sort/environment.yaml +++ b/bio/bedtools/sort/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bedtools =2.29 diff --git a/bio/benchmark/chm-eval-sample/environment.yaml b/bio/benchmark/chm-eval-sample/environment.yaml index 52f624a963..806b882592 100644 --- a/bio/benchmark/chm-eval-sample/environment.yaml +++ b/bio/benchmark/chm-eval-sample/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.10 - curl diff --git a/bio/bgzip/environment.yaml b/bio/bgzip/environment.yaml index bbf6126647..f27f875d41 100644 --- a/bio/bgzip/environment.yaml +++ b/bio/bgzip/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - htslib ==1.12 diff --git a/bio/biobambam2/bamsormadup/environment.yaml b/bio/biobambam2/bamsormadup/environment.yaml index 60bbab986d..f6a2b85063 100644 --- a/bio/biobambam2/bamsormadup/environment.yaml +++ b/bio/biobambam2/bamsormadup/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - biobambam =2.0 diff --git a/bio/bismark/bam2nuc/environment.yaml b/bio/bismark/bam2nuc/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bam2nuc/environment.yaml +++ b/bio/bismark/bam2nuc/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark/environment.yaml b/bio/bismark/bismark/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bismark/environment.yaml +++ b/bio/bismark/bismark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark2bedGraph/environment.yaml b/bio/bismark/bismark2bedGraph/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bismark2bedGraph/environment.yaml +++ b/bio/bismark/bismark2bedGraph/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark2report/environment.yaml b/bio/bismark/bismark2report/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bismark2report/environment.yaml +++ b/bio/bismark/bismark2report/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark2summary/environment.yaml b/bio/bismark/bismark2summary/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bismark2summary/environment.yaml +++ b/bio/bismark/bismark2summary/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark_genome_preparation/environment.yaml b/bio/bismark/bismark_genome_preparation/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/bismark_genome_preparation/environment.yaml +++ b/bio/bismark/bismark_genome_preparation/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/bismark_methylation_extractor/environment.yaml b/bio/bismark/bismark_methylation_extractor/environment.yaml index 3af02da546..6d6eba9baf 100644 --- a/bio/bismark/bismark_methylation_extractor/environment.yaml +++ b/bio/bismark/bismark_methylation_extractor/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/bismark/deduplicate_bismark/environment.yaml b/bio/bismark/deduplicate_bismark/environment.yaml index 565b2e62e4..c2f2faf723 100644 --- a/bio/bismark/deduplicate_bismark/environment.yaml +++ b/bio/bismark/deduplicate_bismark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 ==2.4.2 - bismark ==0.23.0 diff --git a/bio/blast/blastn/environment.yaml b/bio/blast/blastn/environment.yaml index 4780079867..40d601d251 100644 --- a/bio/blast/blastn/environment.yaml +++ b/bio/blast/blastn/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - blast ==2.11 diff --git a/bio/blast/makeblastdb/environment.yaml b/bio/blast/makeblastdb/environment.yaml index 3a3fb4eeb9..81b04be536 100644 --- a/bio/blast/makeblastdb/environment.yaml +++ b/bio/blast/makeblastdb/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - blast ==2.11.0 diff --git a/bio/bowtie2/align/environment.yaml b/bio/bowtie2/align/environment.yaml index f61ba4ace7..af5a77cc00 100644 --- a/bio/bowtie2/align/environment.yaml +++ b/bio/bowtie2/align/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 =2.4 # Keep consistent with version specified in bowtie2/build - samtools =1.14 diff --git a/bio/bowtie2/build/environment.yaml b/bio/bowtie2/build/environment.yaml index 6ff3d49215..c0033ce6d2 100644 --- a/bio/bowtie2/build/environment.yaml +++ b/bio/bowtie2/build/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bowtie2 =2.4 # Keep consistent with version specified in bowtie2/align diff --git a/bio/busco/environment.yaml b/bio/busco/environment.yaml index e717ede351..671319e08f 100644 --- a/bio/busco/environment.yaml +++ b/bio/busco/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - busco==5.1.2 diff --git a/bio/bwa-mem2/index/environment.yaml b/bio/bwa-mem2/index/environment.yaml index 9567db16cb..2d5f4b25d2 100644 --- a/bio/bwa-mem2/index/environment.yaml +++ b/bio/bwa-mem2/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa-mem2 ==2.2.1 diff --git a/bio/bwa-mem2/mem-samblaster/environment.yaml b/bio/bwa-mem2/mem-samblaster/environment.yaml index 454c213582..82c5695d6a 100644 --- a/bio/bwa-mem2/mem-samblaster/environment.yaml +++ b/bio/bwa-mem2/mem-samblaster/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa-mem2 ==2.2.1 - sambamba ==0.7.1 diff --git a/bio/bwa-mem2/mem/environment.yaml b/bio/bwa-mem2/mem/environment.yaml index e3fb88a557..f2db1498e9 100644 --- a/bio/bwa-mem2/mem/environment.yaml +++ b/bio/bwa-mem2/mem/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa-mem2 ==2.2.1 - samtools ==1.12 diff --git a/bio/bwa/aln/environment.yaml b/bio/bwa/aln/environment.yaml index 8b95559739..96143f8b31 100644 --- a/bio/bwa/aln/environment.yaml +++ b/bio/bwa/aln/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa ==0.7.17 diff --git a/bio/bwa/index/environment.yaml b/bio/bwa/index/environment.yaml index 8b95559739..96143f8b31 100644 --- a/bio/bwa/index/environment.yaml +++ b/bio/bwa/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa ==0.7.17 diff --git a/bio/bwa/mem-samblaster/environment.yaml b/bio/bwa/mem-samblaster/environment.yaml index 14d6877ae5..1500b4fa14 100644 --- a/bio/bwa/mem-samblaster/environment.yaml +++ b/bio/bwa/mem-samblaster/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa ==0.7.17 - sambamba ==0.7.1 diff --git a/bio/bwa/mem/environment.yaml b/bio/bwa/mem/environment.yaml index ad572a1dba..b310fd34d8 100644 --- a/bio/bwa/mem/environment.yaml +++ b/bio/bwa/mem/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bwa ==0.7.17 - samtools =1.12 diff --git a/bio/bwa/sampe/environment.yaml b/bio/bwa/sampe/environment.yaml index 37955a515a..4070fcd672 100644 --- a/bio/bwa/sampe/environment.yaml +++ b/bio/bwa/sampe/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bwa ==0.7.17 - samtools ==1.9 diff --git a/bio/bwa/samse/environment.yaml b/bio/bwa/samse/environment.yaml index 37955a515a..4070fcd672 100644 --- a/bio/bwa/samse/environment.yaml +++ b/bio/bwa/samse/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bwa ==0.7.17 - samtools ==1.9 diff --git a/bio/bwa/samxe/environment.yaml b/bio/bwa/samxe/environment.yaml index 37955a515a..4070fcd672 100644 --- a/bio/bwa/samxe/environment.yaml +++ b/bio/bwa/samxe/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bwa ==0.7.17 - samtools ==1.9 diff --git a/bio/clustalo/environment.yaml b/bio/clustalo/environment.yaml index 36f9598163..3be9cee994 100644 --- a/bio/clustalo/environment.yaml +++ b/bio/clustalo/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - clustalo ==1.2.4 diff --git a/bio/cutadapt/pe/environment.yaml b/bio/cutadapt/pe/environment.yaml index 1de836231c..0c50a1b2b5 100644 --- a/bio/cutadapt/pe/environment.yaml +++ b/bio/cutadapt/pe/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - cutadapt ==3.4 diff --git a/bio/cutadapt/se/environment.yaml b/bio/cutadapt/se/environment.yaml index 1de836231c..0c50a1b2b5 100644 --- a/bio/cutadapt/se/environment.yaml +++ b/bio/cutadapt/se/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - cutadapt ==3.4 diff --git a/bio/dada2/add-species/environment.yaml b/bio/dada2/add-species/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/add-species/environment.yaml +++ b/bio/dada2/add-species/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/assign-species/environment.yaml b/bio/dada2/assign-species/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/assign-species/environment.yaml +++ b/bio/dada2/assign-species/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/assign-taxonomy/environment.yaml b/bio/dada2/assign-taxonomy/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/assign-taxonomy/environment.yaml +++ b/bio/dada2/assign-taxonomy/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/collapse-nomismatch/environment.yaml b/bio/dada2/collapse-nomismatch/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/collapse-nomismatch/environment.yaml +++ b/bio/dada2/collapse-nomismatch/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/dereplicate-fastq/environment.yaml b/bio/dada2/dereplicate-fastq/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/dereplicate-fastq/environment.yaml +++ b/bio/dada2/dereplicate-fastq/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/filter-trim/environment.yaml b/bio/dada2/filter-trim/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/filter-trim/environment.yaml +++ b/bio/dada2/filter-trim/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/learn-errors/environment.yaml b/bio/dada2/learn-errors/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/learn-errors/environment.yaml +++ b/bio/dada2/learn-errors/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/make-table/environment.yaml b/bio/dada2/make-table/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/make-table/environment.yaml +++ b/bio/dada2/make-table/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/merge-pairs/environment.yaml b/bio/dada2/merge-pairs/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/merge-pairs/environment.yaml +++ b/bio/dada2/merge-pairs/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/quality-profile/environment.yaml b/bio/dada2/quality-profile/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/quality-profile/environment.yaml +++ b/bio/dada2/quality-profile/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/remove-chimeras/environment.yaml b/bio/dada2/remove-chimeras/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/remove-chimeras/environment.yaml +++ b/bio/dada2/remove-chimeras/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/dada2/sample-inference/environment.yaml b/bio/dada2/sample-inference/environment.yaml index 9be827af98..7fdbe57d7e 100644 --- a/bio/dada2/sample-inference/environment.yaml +++ b/bio/dada2/sample-inference/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-dada2 == 1.16 diff --git a/bio/deeptools/computematrix/environment.yaml b/bio/deeptools/computematrix/environment.yaml index 5241ba07d9..e074c0cb44 100644 --- a/bio/deeptools/computematrix/environment.yaml +++ b/bio/deeptools/computematrix/environment.yaml @@ -1,4 +1,5 @@ channels: - bioconda + - defaults dependencies: - deeptools ==3.4.3 diff --git a/bio/deeptools/plotfingerprint/environment.yaml b/bio/deeptools/plotfingerprint/environment.yaml index 5241ba07d9..e074c0cb44 100644 --- a/bio/deeptools/plotfingerprint/environment.yaml +++ b/bio/deeptools/plotfingerprint/environment.yaml @@ -1,4 +1,5 @@ channels: - bioconda + - defaults dependencies: - deeptools ==3.4.3 diff --git a/bio/deeptools/plotheatmap/environment.yaml b/bio/deeptools/plotheatmap/environment.yaml index 5241ba07d9..e074c0cb44 100644 --- a/bio/deeptools/plotheatmap/environment.yaml +++ b/bio/deeptools/plotheatmap/environment.yaml @@ -1,4 +1,5 @@ channels: - bioconda + - defaults dependencies: - deeptools ==3.4.3 diff --git a/bio/deeptools/plotprofile/environment.yaml b/bio/deeptools/plotprofile/environment.yaml index 5241ba07d9..e074c0cb44 100644 --- a/bio/deeptools/plotprofile/environment.yaml +++ b/bio/deeptools/plotprofile/environment.yaml @@ -1,4 +1,5 @@ channels: - bioconda + - defaults dependencies: - deeptools ==3.4.3 diff --git a/bio/delly/environment.yaml b/bio/delly/environment.yaml index d3fcd82e5e..cadded228b 100644 --- a/bio/delly/environment.yaml +++ b/bio/delly/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - delly ==0.9.1 diff --git a/bio/diamond/blastp/environment.yaml b/bio/diamond/blastp/environment.yaml index a923b6a967..d2afd808ab 100644 --- a/bio/diamond/blastp/environment.yaml +++ b/bio/diamond/blastp/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - diamond==2.0 diff --git a/bio/diamond/blastx/environment.yaml b/bio/diamond/blastx/environment.yaml index b4290ccbce..2782255c68 100644 --- a/bio/diamond/blastx/environment.yaml +++ b/bio/diamond/blastx/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - diamond==2.0.6 diff --git a/bio/diamond/makedb/environment.yaml b/bio/diamond/makedb/environment.yaml index b4290ccbce..2782255c68 100644 --- a/bio/diamond/makedb/environment.yaml +++ b/bio/diamond/makedb/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - diamond==2.0.6 diff --git a/bio/dragmap/align/environment.yaml b/bio/dragmap/align/environment.yaml index 061075f3e4..3413d6261d 100644 --- a/bio/dragmap/align/environment.yaml +++ b/bio/dragmap/align/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - dragmap =1.2 - samtools =1.14 diff --git a/bio/dragmap/build/environment.yaml b/bio/dragmap/build/environment.yaml index 400f1946d3..1fb8e2a3d1 100644 --- a/bio/dragmap/build/environment.yaml +++ b/bio/dragmap/build/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - dragmap =1.2 diff --git a/bio/epic/peaks/environment.yaml b/bio/epic/peaks/environment.yaml index 8a24a5026f..f1680f1729 100644 --- a/bio/epic/peaks/environment.yaml +++ b/bio/epic/peaks/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - epic =0.2.7 - pandas =0.22.0 diff --git a/bio/fastp/environment.yaml b/bio/fastp/environment.yaml index 70d3e322c2..e3798ae3f1 100644 --- a/bio/fastp/environment.yaml +++ b/bio/fastp/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fastp =0.20 diff --git a/bio/fastq_screen/environment.yaml b/bio/fastq_screen/environment.yaml index ac42f97288..54f5b54e19 100644 --- a/bio/fastq_screen/environment.yaml +++ b/bio/fastq_screen/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fastq-screen ==0.5.2 - bowtie2 ==2.2.6 diff --git a/bio/fastqc/environment.yaml b/bio/fastqc/environment.yaml index f4fc5487be..d33cf5b312 100644 --- a/bio/fastqc/environment.yaml +++ b/bio/fastqc/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fastqc ==0.11.9 diff --git a/bio/fasttree/environment.yaml b/bio/fasttree/environment.yaml index 7c1274fd62..ed3de2009b 100644 --- a/bio/fasttree/environment.yaml +++ b/bio/fasttree/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - fasttree ==2.1.10 diff --git a/bio/fgbio/annotatebamwithumis/environment.yaml b/bio/fgbio/annotatebamwithumis/environment.yaml index a4be295f61..32c5d46ab8 100644 --- a/bio/fgbio/annotatebamwithumis/environment.yaml +++ b/bio/fgbio/annotatebamwithumis/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==1.4.0 - snakemake-wrapper-utils ==0.2 diff --git a/bio/fgbio/callmolecularconsensusreads/environment.yaml b/bio/fgbio/callmolecularconsensusreads/environment.yaml index c12aed54de..5fcb2a1f6c 100644 --- a/bio/fgbio/callmolecularconsensusreads/environment.yaml +++ b/bio/fgbio/callmolecularconsensusreads/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==0.6.1 diff --git a/bio/fgbio/collectduplexseqmetrics/environment.yaml b/bio/fgbio/collectduplexseqmetrics/environment.yaml index 9b38dd454b..429745b4ea 100644 --- a/bio/fgbio/collectduplexseqmetrics/environment.yaml +++ b/bio/fgbio/collectduplexseqmetrics/environment.yaml @@ -1,7 +1,8 @@ channels: - r - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==0.6.1 - r-ggplot2 diff --git a/bio/fgbio/filterconsensusreads/environment.yaml b/bio/fgbio/filterconsensusreads/environment.yaml index c12aed54de..5fcb2a1f6c 100644 --- a/bio/fgbio/filterconsensusreads/environment.yaml +++ b/bio/fgbio/filterconsensusreads/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==0.6.1 diff --git a/bio/fgbio/groupreadsbyumi/environment.yaml b/bio/fgbio/groupreadsbyumi/environment.yaml index c12aed54de..5fcb2a1f6c 100644 --- a/bio/fgbio/groupreadsbyumi/environment.yaml +++ b/bio/fgbio/groupreadsbyumi/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==0.6.1 diff --git a/bio/fgbio/setmateinformation/environment.yaml b/bio/fgbio/setmateinformation/environment.yaml index c12aed54de..5fcb2a1f6c 100644 --- a/bio/fgbio/setmateinformation/environment.yaml +++ b/bio/fgbio/setmateinformation/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - fgbio ==0.6.1 diff --git a/bio/freebayes/environment.yaml b/bio/freebayes/environment.yaml index 91ababeb90..dec8279faf 100644 --- a/bio/freebayes/environment.yaml +++ b/bio/freebayes/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - freebayes =1.3.2 - bcftools =1.11 diff --git a/bio/gatk/applybqsr/environment.yaml b/bio/gatk/applybqsr/environment.yaml index 3b4d8e9985..e3b2e9f4d4 100644 --- a/bio/gatk/applybqsr/environment.yaml +++ b/bio/gatk/applybqsr/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/applybqsrspark/environment.yaml b/bio/gatk/applybqsrspark/environment.yaml index 3b4d8e9985..e3b2e9f4d4 100644 --- a/bio/gatk/applybqsrspark/environment.yaml +++ b/bio/gatk/applybqsrspark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/applyvqsr/environment.yaml b/bio/gatk/applyvqsr/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/applyvqsr/environment.yaml +++ b/bio/gatk/applyvqsr/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/baserecalibrator/environment.yaml b/bio/gatk/baserecalibrator/environment.yaml index 3b4d8e9985..e3b2e9f4d4 100644 --- a/bio/gatk/baserecalibrator/environment.yaml +++ b/bio/gatk/baserecalibrator/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/baserecalibratorspark/environment.yaml b/bio/gatk/baserecalibratorspark/environment.yaml index 3b4d8e9985..e3b2e9f4d4 100644 --- a/bio/gatk/baserecalibratorspark/environment.yaml +++ b/bio/gatk/baserecalibratorspark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/cleansam/environment.yaml b/bio/gatk/cleansam/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/cleansam/environment.yaml +++ b/bio/gatk/cleansam/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/combinegvcfs/environment.yaml b/bio/gatk/combinegvcfs/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/combinegvcfs/environment.yaml +++ b/bio/gatk/combinegvcfs/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/estimatelibrarycomplexity/environment.yaml b/bio/gatk/estimatelibrarycomplexity/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/estimatelibrarycomplexity/environment.yaml +++ b/bio/gatk/estimatelibrarycomplexity/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/filtermutectcalls/environment.yaml b/bio/gatk/filtermutectcalls/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/filtermutectcalls/environment.yaml +++ b/bio/gatk/filtermutectcalls/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/genomicsdbimport/environment.yaml b/bio/gatk/genomicsdbimport/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/genomicsdbimport/environment.yaml +++ b/bio/gatk/genomicsdbimport/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/genotypegvcfs/environment.yaml b/bio/gatk/genotypegvcfs/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/genotypegvcfs/environment.yaml +++ b/bio/gatk/genotypegvcfs/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/haplotypecaller/environment.yaml b/bio/gatk/haplotypecaller/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/haplotypecaller/environment.yaml +++ b/bio/gatk/haplotypecaller/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/intervallisttobed/environment.yaml b/bio/gatk/intervallisttobed/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/intervallisttobed/environment.yaml +++ b/bio/gatk/intervallisttobed/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/markduplicatesspark/environment.yaml b/bio/gatk/markduplicatesspark/environment.yaml index 3b4d8e9985..e3b2e9f4d4 100644 --- a/bio/gatk/markduplicatesspark/environment.yaml +++ b/bio/gatk/markduplicatesspark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/mutect/environment.yaml b/bio/gatk/mutect/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/mutect/environment.yaml +++ b/bio/gatk/mutect/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/printreadsspark/environment.yaml b/bio/gatk/printreadsspark/environment.yaml index 30b018d17d..2050b8aec9 100644 --- a/bio/gatk/printreadsspark/environment.yaml +++ b/bio/gatk/printreadsspark/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - openjdk =8 diff --git a/bio/gatk/scatterintervalsbyns/environment.yaml b/bio/gatk/scatterintervalsbyns/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/scatterintervalsbyns/environment.yaml +++ b/bio/gatk/scatterintervalsbyns/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/selectvariants/environment.yaml b/bio/gatk/selectvariants/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/selectvariants/environment.yaml +++ b/bio/gatk/selectvariants/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/splitncigarreads/environment.yaml b/bio/gatk/splitncigarreads/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/splitncigarreads/environment.yaml +++ b/bio/gatk/splitncigarreads/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/variantannotator/environment.yaml b/bio/gatk/variantannotator/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/variantannotator/environment.yaml +++ b/bio/gatk/variantannotator/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/varianteval/environment.yaml b/bio/gatk/varianteval/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/varianteval/environment.yaml +++ b/bio/gatk/varianteval/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/variantfiltration/environment.yaml b/bio/gatk/variantfiltration/environment.yaml index 701d059e79..c43a093b7b 100644 --- a/bio/gatk/variantfiltration/environment.yaml +++ b/bio/gatk/variantfiltration/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk/variantrecalibrator/environment.yaml b/bio/gatk/variantrecalibrator/environment.yaml index 44e2902e29..9d8031a635 100644 --- a/bio/gatk/variantrecalibrator/environment.yaml +++ b/bio/gatk/variantrecalibrator/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk4 =4.2 - snakemake-wrapper-utils =0.3 diff --git a/bio/gatk3/baserecalibrator/environment.yaml b/bio/gatk3/baserecalibrator/environment.yaml index 9e1c563aa8..87fe20c0d1 100644 --- a/bio/gatk3/baserecalibrator/environment.yaml +++ b/bio/gatk3/baserecalibrator/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk ==3.8 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/gatk3/indelrealigner/environment.yaml b/bio/gatk3/indelrealigner/environment.yaml index 9e1c563aa8..87fe20c0d1 100644 --- a/bio/gatk3/indelrealigner/environment.yaml +++ b/bio/gatk3/indelrealigner/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk ==3.8 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/gatk3/printreads/environment.yaml b/bio/gatk3/printreads/environment.yaml index 9e1c563aa8..87fe20c0d1 100644 --- a/bio/gatk3/printreads/environment.yaml +++ b/bio/gatk3/printreads/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk ==3.8 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/gatk3/realignertargetcreator/environment.yaml b/bio/gatk3/realignertargetcreator/environment.yaml index 9e1c563aa8..87fe20c0d1 100644 --- a/bio/gatk3/realignertargetcreator/environment.yaml +++ b/bio/gatk3/realignertargetcreator/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gatk ==3.8 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/gdc-client/download/environment.yaml b/bio/gdc-client/download/environment.yaml index 194ed5e13c..632d54c2d7 100644 --- a/bio/gdc-client/download/environment.yaml +++ b/bio/gdc-client/download/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - gdc-client ==1.5.0 diff --git a/bio/genomepy/environment.yaml b/bio/genomepy/environment.yaml index 76fc46ae40..8ae3f32639 100644 --- a/bio/genomepy/environment.yaml +++ b/bio/genomepy/environment.yaml @@ -1,5 +1,6 @@ channels: - bioconda + - defaults - conda-forge dependencies: - bioconda::genomepy==0.8.3 diff --git a/bio/gridss/assemble/environment.yaml b/bio/gridss/assemble/environment.yaml index ec54f6cc22..da0e822664 100644 --- a/bio/gridss/assemble/environment.yaml +++ b/bio/gridss/assemble/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gridss ==2.9.4 diff --git a/bio/gridss/call/environment.yaml b/bio/gridss/call/environment.yaml index f951367426..7a96c96ab4 100644 --- a/bio/gridss/call/environment.yaml +++ b/bio/gridss/call/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gridss ==2.9.4 - cpulimit =0.2 diff --git a/bio/gridss/preprocess/environment.yaml b/bio/gridss/preprocess/environment.yaml index ec54f6cc22..da0e822664 100644 --- a/bio/gridss/preprocess/environment.yaml +++ b/bio/gridss/preprocess/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gridss ==2.9.4 diff --git a/bio/gridss/setupreference/environment.yaml b/bio/gridss/setupreference/environment.yaml index ec54f6cc22..da0e822664 100644 --- a/bio/gridss/setupreference/environment.yaml +++ b/bio/gridss/setupreference/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - gridss ==2.9.4 diff --git a/bio/hap.py/hap.py/environment.yaml b/bio/hap.py/hap.py/environment.yaml index 0bba4b22f1..2e82af629a 100644 --- a/bio/hap.py/hap.py/environment.yaml +++ b/bio/hap.py/hap.py/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - hap.py ==0.3.14 - rtg-tools ==3.10.1 diff --git a/bio/hap.py/pre.py/environment.yaml b/bio/hap.py/pre.py/environment.yaml index ac2722fa94..ed41dba0e9 100644 --- a/bio/hap.py/pre.py/environment.yaml +++ b/bio/hap.py/pre.py/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - hap.py =0.3.14 diff --git a/bio/hisat2/align/environment.yaml b/bio/hisat2/align/environment.yaml index 7f72229a18..02562f8aaf 100644 --- a/bio/hisat2/align/environment.yaml +++ b/bio/hisat2/align/environment.yaml @@ -1,5 +1,6 @@ channels: - bioconda + - defaults dependencies: - hisat2 ==2.1.0 - samtools ==1.9 diff --git a/bio/hisat2/index/environment.yaml b/bio/hisat2/index/environment.yaml index 7f72229a18..02562f8aaf 100644 --- a/bio/hisat2/index/environment.yaml +++ b/bio/hisat2/index/environment.yaml @@ -1,5 +1,6 @@ channels: - bioconda + - defaults dependencies: - hisat2 ==2.1.0 - samtools ==1.9 diff --git a/bio/hmmer/hmmbuild/environment.yaml b/bio/hmmer/hmmbuild/environment.yaml index 661b7eb8b9..8507c129ff 100644 --- a/bio/hmmer/hmmbuild/environment.yaml +++ b/bio/hmmer/hmmbuild/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - hmmer=3.2.1 diff --git a/bio/hmmer/hmmpress/environment.yaml b/bio/hmmer/hmmpress/environment.yaml index 661b7eb8b9..8507c129ff 100644 --- a/bio/hmmer/hmmpress/environment.yaml +++ b/bio/hmmer/hmmpress/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - hmmer=3.2.1 diff --git a/bio/hmmer/hmmscan/environment.yaml b/bio/hmmer/hmmscan/environment.yaml index 661b7eb8b9..8507c129ff 100644 --- a/bio/hmmer/hmmscan/environment.yaml +++ b/bio/hmmer/hmmscan/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - hmmer=3.2.1 diff --git a/bio/hmmer/hmmsearch/environment.yaml b/bio/hmmer/hmmsearch/environment.yaml index 661b7eb8b9..8507c129ff 100644 --- a/bio/hmmer/hmmsearch/environment.yaml +++ b/bio/hmmer/hmmsearch/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - hmmer=3.2.1 diff --git a/bio/homer/annotatePeaks/environment.yaml b/bio/homer/annotatePeaks/environment.yaml index 9677c878c7..eaa7b718b5 100644 --- a/bio/homer/annotatePeaks/environment.yaml +++ b/bio/homer/annotatePeaks/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - homer ==4.11 diff --git a/bio/homer/findPeaks/environment.yaml b/bio/homer/findPeaks/environment.yaml index 9677c878c7..eaa7b718b5 100644 --- a/bio/homer/findPeaks/environment.yaml +++ b/bio/homer/findPeaks/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - homer ==4.11 diff --git a/bio/homer/getDifferentialPeaks/environment.yaml b/bio/homer/getDifferentialPeaks/environment.yaml index 9677c878c7..eaa7b718b5 100644 --- a/bio/homer/getDifferentialPeaks/environment.yaml +++ b/bio/homer/getDifferentialPeaks/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - homer ==4.11 diff --git a/bio/homer/makeTagDirectory/environment.yaml b/bio/homer/makeTagDirectory/environment.yaml index 2bc3a3e023..aed0ce9d98 100644 --- a/bio/homer/makeTagDirectory/environment.yaml +++ b/bio/homer/makeTagDirectory/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - homer ==4.11 - samtools ==1.10 diff --git a/bio/homer/mergePeaks/environment.yaml b/bio/homer/mergePeaks/environment.yaml index 9677c878c7..eaa7b718b5 100644 --- a/bio/homer/mergePeaks/environment.yaml +++ b/bio/homer/mergePeaks/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - homer ==4.11 diff --git a/bio/infernal/cmpress/environment.yaml b/bio/infernal/cmpress/environment.yaml index 8d0bb4c07a..e17fa81d20 100644 --- a/bio/infernal/cmpress/environment.yaml +++ b/bio/infernal/cmpress/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - infernal=1.1.2 diff --git a/bio/infernal/cmscan/environment.yaml b/bio/infernal/cmscan/environment.yaml index 8d0bb4c07a..e17fa81d20 100644 --- a/bio/infernal/cmscan/environment.yaml +++ b/bio/infernal/cmscan/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - infernal=1.1.2 diff --git a/bio/jannovar/environment.yaml b/bio/jannovar/environment.yaml index a819dd2372..51e9634aa2 100644 --- a/bio/jannovar/environment.yaml +++ b/bio/jannovar/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - jannovar-cli ==0.31 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/jellyfish/count/environment.yaml b/bio/jellyfish/count/environment.yaml index b031972a21..174c237d4b 100644 --- a/bio/jellyfish/count/environment.yaml +++ b/bio/jellyfish/count/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kmer-jellyfish==2.3 diff --git a/bio/jellyfish/dump/environment.yaml b/bio/jellyfish/dump/environment.yaml index b031972a21..174c237d4b 100644 --- a/bio/jellyfish/dump/environment.yaml +++ b/bio/jellyfish/dump/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kmer-jellyfish==2.3 diff --git a/bio/jellyfish/histo/environment.yaml b/bio/jellyfish/histo/environment.yaml index b031972a21..174c237d4b 100644 --- a/bio/jellyfish/histo/environment.yaml +++ b/bio/jellyfish/histo/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kmer-jellyfish==2.3 diff --git a/bio/jellyfish/merge/environment.yaml b/bio/jellyfish/merge/environment.yaml index b031972a21..174c237d4b 100644 --- a/bio/jellyfish/merge/environment.yaml +++ b/bio/jellyfish/merge/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kmer-jellyfish==2.3 diff --git a/bio/kallisto/index/environment.yaml b/bio/kallisto/index/environment.yaml index dfee735b31..38b3ef69f0 100644 --- a/bio/kallisto/index/environment.yaml +++ b/bio/kallisto/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kallisto ==0.45.0 diff --git a/bio/kallisto/quant/environment.yaml b/bio/kallisto/quant/environment.yaml index dfee735b31..38b3ef69f0 100644 --- a/bio/kallisto/quant/environment.yaml +++ b/bio/kallisto/quant/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - kallisto ==0.45.0 diff --git a/bio/last/lastal/environment.yaml b/bio/last/lastal/environment.yaml index d85edeb3f2..7653a68fb6 100644 --- a/bio/last/lastal/environment.yaml +++ b/bio/last/lastal/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - last=874 diff --git a/bio/last/lastdb/environment.yaml b/bio/last/lastdb/environment.yaml index d85edeb3f2..7653a68fb6 100644 --- a/bio/last/lastdb/environment.yaml +++ b/bio/last/lastdb/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - last=874 diff --git a/bio/liftoff/environment.yaml b/bio/liftoff/environment.yaml index daa0fdf63a..9ad89a5257 100644 --- a/bio/liftoff/environment.yaml +++ b/bio/liftoff/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - liftoff =1.6 diff --git a/bio/lofreq/call/environment.yaml b/bio/lofreq/call/environment.yaml index e737a3a7db..f54dfdc37e 100644 --- a/bio/lofreq/call/environment.yaml +++ b/bio/lofreq/call/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools ==1.6 - lofreq ==2.1.3.1 diff --git a/bio/macs2/callpeak/environment.yaml b/bio/macs2/callpeak/environment.yaml index cc5e0a9aa9..7ad087a335 100644 --- a/bio/macs2/callpeak/environment.yaml +++ b/bio/macs2/callpeak/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - macs2>=2.2 diff --git a/bio/manta/environment.yaml b/bio/manta/environment.yaml index 280f7b53e8..8bf65aa111 100644 --- a/bio/manta/environment.yaml +++ b/bio/manta/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - manta=1.6 - bcftools=1.14 diff --git a/bio/mapdamage2/environment.yaml b/bio/mapdamage2/environment.yaml index 11ae8cd8ea..509d488e2b 100644 --- a/bio/mapdamage2/environment.yaml +++ b/bio/mapdamage2/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - mapdamage2 =2.2 - python >=3.9 diff --git a/bio/mashmap/environment.yaml b/bio/mashmap/environment.yaml index bca9873f5e..5aefedc170 100644 --- a/bio/mashmap/environment.yaml +++ b/bio/mashmap/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - mashmap =2.0 - gsl =2.7 diff --git a/bio/microphaser/build_reference/environment.yaml b/bio/microphaser/build_reference/environment.yaml index 1698595d48..3237608c1a 100644 --- a/bio/microphaser/build_reference/environment.yaml +++ b/bio/microphaser/build_reference/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - microphaser =0.4 diff --git a/bio/microphaser/filter/environment.yaml b/bio/microphaser/filter/environment.yaml index 1698595d48..3237608c1a 100644 --- a/bio/microphaser/filter/environment.yaml +++ b/bio/microphaser/filter/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - microphaser =0.4 diff --git a/bio/microphaser/normal/environment.yaml b/bio/microphaser/normal/environment.yaml index 8b95b68c8b..a32712580d 100644 --- a/bio/microphaser/normal/environment.yaml +++ b/bio/microphaser/normal/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - microphaser =0.3 diff --git a/bio/microphaser/somatic/environment.yaml b/bio/microphaser/somatic/environment.yaml index 8b95b68c8b..a32712580d 100644 --- a/bio/microphaser/somatic/environment.yaml +++ b/bio/microphaser/somatic/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - microphaser =0.3 diff --git a/bio/minimap2/aligner/environment.yaml b/bio/minimap2/aligner/environment.yaml index 78597fd678..60ce9c9ca5 100644 --- a/bio/minimap2/aligner/environment.yaml +++ b/bio/minimap2/aligner/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - minimap2 ==2.17 - samtools ==1.12 diff --git a/bio/minimap2/index/environment.yaml b/bio/minimap2/index/environment.yaml index 8a1533bc72..2ea9e7d429 100644 --- a/bio/minimap2/index/environment.yaml +++ b/bio/minimap2/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - minimap2 ==2.17 diff --git a/bio/mlst/environment.yaml b/bio/mlst/environment.yaml index 179e684c8a..7325cfa23e 100644 --- a/bio/mlst/environment.yaml +++ b/bio/mlst/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - mlst =2.19 diff --git a/bio/mosdepth/environment.yaml b/bio/mosdepth/environment.yaml index 9242d23bef..f9a66f310e 100644 --- a/bio/mosdepth/environment.yaml +++ b/bio/mosdepth/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - mosdepth ==0.3.1 diff --git a/bio/msisensor/msi/environment.yaml b/bio/msisensor/msi/environment.yaml index 616419e8e6..6e99077636 100644 --- a/bio/msisensor/msi/environment.yaml +++ b/bio/msisensor/msi/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - msisensor ==0.5 diff --git a/bio/msisensor/scan/environment.yaml b/bio/msisensor/scan/environment.yaml index 616419e8e6..6e99077636 100644 --- a/bio/msisensor/scan/environment.yaml +++ b/bio/msisensor/scan/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - msisensor ==0.5 diff --git a/bio/multiqc/environment.yaml b/bio/multiqc/environment.yaml index fb91ae8ba5..34ea6df1dc 100644 --- a/bio/multiqc/environment.yaml +++ b/bio/multiqc/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - multiqc =1.12 diff --git a/bio/muscle/environment.yaml b/bio/muscle/environment.yaml index 2c2582bfb1..cdbd03e20a 100644 --- a/bio/muscle/environment.yaml +++ b/bio/muscle/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - muscle ==3.8.1551 diff --git a/bio/nanosim-h/environment.yaml b/bio/nanosim-h/environment.yaml index ecd3dfad91..a6bf9452c9 100644 --- a/bio/nanosim-h/environment.yaml +++ b/bio/nanosim-h/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - nanosim-h ==1.1.0.4 diff --git a/bio/ngs-disambiguate/environment.yaml b/bio/ngs-disambiguate/environment.yaml index d826fd6756..bd8ff07b0b 100644 --- a/bio/ngs-disambiguate/environment.yaml +++ b/bio/ngs-disambiguate/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ngs-disambiguate ==2016.11.10 - bamtools ==2.4.0 diff --git a/bio/optitype/environment.yaml b/bio/optitype/environment.yaml index 8b7458aa0e..ae8bb27ebb 100644 --- a/bio/optitype/environment.yaml +++ b/bio/optitype/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - optitype ==1.3.5 diff --git a/bio/paladin/align/environment.yaml b/bio/paladin/align/environment.yaml index 4f6e409072..87c82439a8 100644 --- a/bio/paladin/align/environment.yaml +++ b/bio/paladin/align/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - paladin=1.4.4 - samtools=1.5 diff --git a/bio/paladin/index/environment.yaml b/bio/paladin/index/environment.yaml index 4f6e409072..87c82439a8 100644 --- a/bio/paladin/index/environment.yaml +++ b/bio/paladin/index/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - paladin=1.4.4 - samtools=1.5 diff --git a/bio/paladin/prepare/environment.yaml b/bio/paladin/prepare/environment.yaml index 4f6e409072..87c82439a8 100644 --- a/bio/paladin/prepare/environment.yaml +++ b/bio/paladin/prepare/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - paladin=1.4.4 - samtools=1.5 diff --git a/bio/pandora/index/environment.yaml b/bio/pandora/index/environment.yaml index 4913870a7d..ac98f2e51b 100644 --- a/bio/pandora/index/environment.yaml +++ b/bio/pandora/index/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - pandora =0.9 diff --git a/bio/pbmm2/align/environment.yaml b/bio/pbmm2/align/environment.yaml index 1c97d4b081..3f6b2f8559 100644 --- a/bio/pbmm2/align/environment.yaml +++ b/bio/pbmm2/align/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - pbmm2 ==1.4.0 diff --git a/bio/pbmm2/index/environment.yaml b/bio/pbmm2/index/environment.yaml index 53c006e7f0..e7ba8f9e06 100644 --- a/bio/pbmm2/index/environment.yaml +++ b/bio/pbmm2/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - pbmm2 ==1.3.0 diff --git a/bio/pear/environment.yaml b/bio/pear/environment.yaml index 78fa2c9cb4..c71784f629 100644 --- a/bio/pear/environment.yaml +++ b/bio/pear/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - pear=0.9.6 diff --git a/bio/picard/addorreplacereadgroups/environment.yaml b/bio/picard/addorreplacereadgroups/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/addorreplacereadgroups/environment.yaml +++ b/bio/picard/addorreplacereadgroups/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/bedtointervallist/environment.yaml b/bio/picard/bedtointervallist/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/bedtointervallist/environment.yaml +++ b/bio/picard/bedtointervallist/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collectalignmentsummarymetrics/environment.yaml b/bio/picard/collectalignmentsummarymetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collectalignmentsummarymetrics/environment.yaml +++ b/bio/picard/collectalignmentsummarymetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collectgcbiasmetrics/environment.yaml b/bio/picard/collectgcbiasmetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collectgcbiasmetrics/environment.yaml +++ b/bio/picard/collectgcbiasmetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collecthsmetrics/environment.yaml b/bio/picard/collecthsmetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collecthsmetrics/environment.yaml +++ b/bio/picard/collecthsmetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collectinsertsizemetrics/environment.yaml b/bio/picard/collectinsertsizemetrics/environment.yaml index 89477f9852..c674ec930d 100644 --- a/bio/picard/collectinsertsizemetrics/environment.yaml +++ b/bio/picard/collectinsertsizemetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - r-base ==3.6.2 diff --git a/bio/picard/collectmultiplemetrics/environment.yaml b/bio/picard/collectmultiplemetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collectmultiplemetrics/environment.yaml +++ b/bio/picard/collectmultiplemetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collectrnaseqmetrics/environment.yaml b/bio/picard/collectrnaseqmetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collectrnaseqmetrics/environment.yaml +++ b/bio/picard/collectrnaseqmetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/collecttargetedpcrmetrics/environment.yaml b/bio/picard/collecttargetedpcrmetrics/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/collecttargetedpcrmetrics/environment.yaml +++ b/bio/picard/collecttargetedpcrmetrics/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/createsequencedictionary/environment.yaml b/bio/picard/createsequencedictionary/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/createsequencedictionary/environment.yaml +++ b/bio/picard/createsequencedictionary/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/markduplicates/environment.yaml b/bio/picard/markduplicates/environment.yaml index d1742454a6..961dfd2840 100644 --- a/bio/picard/markduplicates/environment.yaml +++ b/bio/picard/markduplicates/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - samtools =1.15 diff --git a/bio/picard/markduplicateswithmatecigar/environment.yaml b/bio/picard/markduplicateswithmatecigar/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/markduplicateswithmatecigar/environment.yaml +++ b/bio/picard/markduplicateswithmatecigar/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/mergesamfiles/environment.yaml b/bio/picard/mergesamfiles/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/mergesamfiles/environment.yaml +++ b/bio/picard/mergesamfiles/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/mergevcfs/environment.yaml b/bio/picard/mergevcfs/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/mergevcfs/environment.yaml +++ b/bio/picard/mergevcfs/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/revertsam/environment.yaml b/bio/picard/revertsam/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/revertsam/environment.yaml +++ b/bio/picard/revertsam/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/samtofastq/environment.yaml b/bio/picard/samtofastq/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/samtofastq/environment.yaml +++ b/bio/picard/samtofastq/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/picard/sortsam/environment.yaml b/bio/picard/sortsam/environment.yaml index ded7a83c21..a5d0ec5387 100644 --- a/bio/picard/sortsam/environment.yaml +++ b/bio/picard/sortsam/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - picard =2.27 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/pindel/call/environment.yaml b/bio/pindel/call/environment.yaml index 76f9773b8b..05eb293e33 100644 --- a/bio/pindel/call/environment.yaml +++ b/bio/pindel/call/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - pindel ==0.2.5b8 diff --git a/bio/pindel/pindel2vcf/environment.yaml b/bio/pindel/pindel2vcf/environment.yaml index 76f9773b8b..05eb293e33 100644 --- a/bio/pindel/pindel2vcf/environment.yaml +++ b/bio/pindel/pindel2vcf/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - pindel ==0.2.5b8 diff --git a/bio/plass/environment.yaml b/bio/plass/environment.yaml index 80c9f5aa2a..64d3486e61 100644 --- a/bio/plass/environment.yaml +++ b/bio/plass/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - plass=2.c7e35 diff --git a/bio/prosolo/control-fdr/environment.yaml b/bio/prosolo/control-fdr/environment.yaml index b09f0b9435..edb686a52d 100644 --- a/bio/prosolo/control-fdr/environment.yaml +++ b/bio/prosolo/control-fdr/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - prosolo ==0.6.1 diff --git a/bio/prosolo/single-cell-bulk/environment.yaml b/bio/prosolo/single-cell-bulk/environment.yaml index b09f0b9435..edb686a52d 100644 --- a/bio/prosolo/single-cell-bulk/environment.yaml +++ b/bio/prosolo/single-cell-bulk/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - prosolo ==0.6.1 diff --git a/bio/ptrimmer/environment.yaml b/bio/ptrimmer/environment.yaml index b077ff74b3..fa7ea7c6b8 100644 --- a/bio/ptrimmer/environment.yaml +++ b/bio/ptrimmer/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - ptrimmer ==1.3.3 \ No newline at end of file diff --git a/bio/qualimap/rnaseq/environment.yaml b/bio/qualimap/rnaseq/environment.yaml index 60d6c2de78..459805a49e 100644 --- a/bio/qualimap/rnaseq/environment.yaml +++ b/bio/qualimap/rnaseq/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - qualimap ==2.2.2d - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/rasusa/environment.yaml b/bio/rasusa/environment.yaml index 2796cd76f8..af9059820d 100644 --- a/bio/rasusa/environment.yaml +++ b/bio/rasusa/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - rasusa =0.6 diff --git a/bio/razers3/environment.yaml b/bio/razers3/environment.yaml index 0b23725e84..7c65ef6924 100644 --- a/bio/razers3/environment.yaml +++ b/bio/razers3/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda + - defaults dependencies: - razers3 ==3.5.8 diff --git a/bio/rbt/csvreport/environment.yaml b/bio/rbt/csvreport/environment.yaml index 64092dbf54..d343b11788 100644 --- a/bio/rbt/csvreport/environment.yaml +++ b/bio/rbt/csvreport/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - rust-bio-tools =0.22 diff --git a/bio/rebaler/environment.yaml b/bio/rebaler/environment.yaml index 2c777bafd5..12660406a5 100644 --- a/bio/rebaler/environment.yaml +++ b/bio/rebaler/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - rebaler ==0.2.0 diff --git a/bio/reference/ensembl-variation/environment.yaml b/bio/reference/ensembl-variation/environment.yaml index 4238782738..14764f5c21 100644 --- a/bio/reference/ensembl-variation/environment.yaml +++ b/bio/reference/ensembl-variation/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bcftools =1.11 - curl diff --git a/bio/refgenie/environment.yaml b/bio/refgenie/environment.yaml index d7b1c377ca..06d40e3ed0 100644 --- a/bio/refgenie/environment.yaml +++ b/bio/refgenie/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - refgenie =0.9.2 - refgenconf =0.9.0 diff --git a/bio/salmon/decoys/environment.yaml b/bio/salmon/decoys/environment.yaml index d3bfb01181..0c482bd7f3 100644 --- a/bio/salmon/decoys/environment.yaml +++ b/bio/salmon/decoys/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge + - defaults dependencies: - bzip2 =1.0.8 - gzip =1.12 diff --git a/bio/salmon/index/environment.yaml b/bio/salmon/index/environment.yaml index cc4861db82..4f96d1028d 100644 --- a/bio/salmon/index/environment.yaml +++ b/bio/salmon/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - salmon ==1.8.0 diff --git a/bio/salmon/quant/environment.yaml b/bio/salmon/quant/environment.yaml index d629ab0050..8670e957bd 100644 --- a/bio/salmon/quant/environment.yaml +++ b/bio/salmon/quant/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - salmon ==1.8.0 - gzip ==1.11 diff --git a/bio/sambamba/flagstat/environment.yaml b/bio/sambamba/flagstat/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/flagstat/environment.yaml +++ b/bio/sambamba/flagstat/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/index/environment.yaml b/bio/sambamba/index/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/index/environment.yaml +++ b/bio/sambamba/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/markdup/environment.yaml b/bio/sambamba/markdup/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/markdup/environment.yaml +++ b/bio/sambamba/markdup/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/merge/environment.yaml b/bio/sambamba/merge/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/merge/environment.yaml +++ b/bio/sambamba/merge/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/slice/environment.yaml b/bio/sambamba/slice/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/slice/environment.yaml +++ b/bio/sambamba/slice/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/sort/environment.yaml b/bio/sambamba/sort/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/sort/environment.yaml +++ b/bio/sambamba/sort/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/sambamba/view/environment.yaml b/bio/sambamba/view/environment.yaml index 0eeaf74726..80f9a7f290 100644 --- a/bio/sambamba/view/environment.yaml +++ b/bio/sambamba/view/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sambamba ==0.8.0 diff --git a/bio/samtools/calmd/environment.yaml b/bio/samtools/calmd/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/calmd/environment.yaml +++ b/bio/samtools/calmd/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/depth/environment.yaml b/bio/samtools/depth/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/depth/environment.yaml +++ b/bio/samtools/depth/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/faidx/environment.yaml b/bio/samtools/faidx/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/faidx/environment.yaml +++ b/bio/samtools/faidx/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/fastx/environment.yaml b/bio/samtools/fastx/environment.yaml index ffe9b8b5e9..a3d9c7ae01 100644 --- a/bio/samtools/fastx/environment.yaml +++ b/bio/samtools/fastx/environment.yaml @@ -1,7 +1,8 @@ name: samtools channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/fixmate/environment.yaml b/bio/samtools/fixmate/environment.yaml index ffe9b8b5e9..a3d9c7ae01 100644 --- a/bio/samtools/fixmate/environment.yaml +++ b/bio/samtools/fixmate/environment.yaml @@ -1,7 +1,8 @@ name: samtools channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/flagstat/environment.yaml b/bio/samtools/flagstat/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/flagstat/environment.yaml +++ b/bio/samtools/flagstat/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/idxstats/environment.yaml b/bio/samtools/idxstats/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/idxstats/environment.yaml +++ b/bio/samtools/idxstats/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/index/environment.yaml b/bio/samtools/index/environment.yaml index de5459dd29..8de8caf4e2 100644 --- a/bio/samtools/index/environment.yaml +++ b/bio/samtools/index/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 diff --git a/bio/samtools/merge/environment.yaml b/bio/samtools/merge/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/merge/environment.yaml +++ b/bio/samtools/merge/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/mpileup/environment.yaml b/bio/samtools/mpileup/environment.yaml index d3ee40cd14..496ce9a972 100644 --- a/bio/samtools/mpileup/environment.yaml +++ b/bio/samtools/mpileup/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - pigz =2.6 diff --git a/bio/samtools/sort/environment.yaml b/bio/samtools/sort/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/sort/environment.yaml +++ b/bio/samtools/sort/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/samtools/stats/environment.yaml b/bio/samtools/stats/environment.yaml index d8d8154bf2..7d855ab3b3 100644 --- a/bio/samtools/stats/environment.yaml +++ b/bio/samtools/stats/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools=1.14 - snakemake-wrapper-utils=0.3 diff --git a/bio/samtools/view/environment.yaml b/bio/samtools/view/environment.yaml index 561b29cd22..9d771f82ec 100644 --- a/bio/samtools/view/environment.yaml +++ b/bio/samtools/view/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - samtools =1.14 - snakemake-wrapper-utils =0.3 diff --git a/bio/seqtk/mergepe/environment.yaml b/bio/seqtk/mergepe/environment.yaml index 6e988807f8..80a74836fd 100644 --- a/bio/seqtk/mergepe/environment.yaml +++ b/bio/seqtk/mergepe/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - seqtk =1.3 - pigz =2.3 diff --git a/bio/seqtk/seq/environment.yaml b/bio/seqtk/seq/environment.yaml index 5d0624f821..b0be2c88b3 100644 --- a/bio/seqtk/seq/environment.yaml +++ b/bio/seqtk/seq/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - seqtk ==1.3 diff --git a/bio/seqtk/subsample/pe/environment.yaml b/bio/seqtk/subsample/pe/environment.yaml index 64485f2ad8..663305480a 100644 --- a/bio/seqtk/subsample/pe/environment.yaml +++ b/bio/seqtk/subsample/pe/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - seqtk ==1.3 - pigz =2.3 diff --git a/bio/seqtk/subsample/se/environment.yaml b/bio/seqtk/subsample/se/environment.yaml index 64485f2ad8..663305480a 100644 --- a/bio/seqtk/subsample/se/environment.yaml +++ b/bio/seqtk/subsample/se/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - seqtk ==1.3 - pigz =2.3 diff --git a/bio/shovill/environment.yaml b/bio/shovill/environment.yaml index 4c50ad72e8..5a0b25e880 100644 --- a/bio/shovill/environment.yaml +++ b/bio/shovill/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - shovill ==1.1.0 diff --git a/bio/sickle/pe/environment.yaml b/bio/sickle/pe/environment.yaml index 5a536fb12e..36affaa831 100644 --- a/bio/sickle/pe/environment.yaml +++ b/bio/sickle/pe/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sickle-trim ==1.33 diff --git a/bio/sickle/se/environment.yaml b/bio/sickle/se/environment.yaml index 5a536fb12e..36affaa831 100644 --- a/bio/sickle/se/environment.yaml +++ b/bio/sickle/se/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sickle-trim ==1.33 diff --git a/bio/snp-mutator/environment.yaml b/bio/snp-mutator/environment.yaml index cb73de2c48..d789797b12 100644 --- a/bio/snp-mutator/environment.yaml +++ b/bio/snp-mutator/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snp-mutator ==1.2.0 diff --git a/bio/snpeff/annotate/environment.yaml b/bio/snpeff/annotate/environment.yaml index f967f42c35..5f6a9c2c04 100644 --- a/bio/snpeff/annotate/environment.yaml +++ b/bio/snpeff/annotate/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpeff ==4.3.1t - bcftools =1.11 diff --git a/bio/snpeff/download/environment.yaml b/bio/snpeff/download/environment.yaml index f967f42c35..5f6a9c2c04 100644 --- a/bio/snpeff/download/environment.yaml +++ b/bio/snpeff/download/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpeff ==4.3.1t - bcftools =1.11 diff --git a/bio/snpsift/annotate/environment.yaml b/bio/snpsift/annotate/environment.yaml index 6fb9108754..1e63b8350d 100644 --- a/bio/snpsift/annotate/environment.yaml +++ b/bio/snpsift/annotate/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpsift ==4.3.1t - bcftools ==1.10.2 diff --git a/bio/snpsift/dbnsfp/environment.yaml b/bio/snpsift/dbnsfp/environment.yaml index f77fc43337..6aaa4fcf4a 100644 --- a/bio/snpsift/dbnsfp/environment.yaml +++ b/bio/snpsift/dbnsfp/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpsift=4.3.1t - bcftools ==1.10.2 diff --git a/bio/snpsift/genesets/environment.yaml b/bio/snpsift/genesets/environment.yaml index 8b747acb8e..e5911a684a 100644 --- a/bio/snpsift/genesets/environment.yaml +++ b/bio/snpsift/genesets/environment.yaml @@ -1,7 +1,7 @@ name: snpsift channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpsift ==4.3.1t - bcftools ==1.10.2 diff --git a/bio/snpsift/gwascat/environment.yaml b/bio/snpsift/gwascat/environment.yaml index f59701617c..279b5f8649 100644 --- a/bio/snpsift/gwascat/environment.yaml +++ b/bio/snpsift/gwascat/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpsift ==4.3.1t - bcftools ==1.10.2 diff --git a/bio/snpsift/varType/environment.yaml b/bio/snpsift/varType/environment.yaml index 891ca0081e..23e47baad5 100644 --- a/bio/snpsift/varType/environment.yaml +++ b/bio/snpsift/varType/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - snpsift =4.3.1t - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/sourmash/compute/environment.yaml b/bio/sourmash/compute/environment.yaml index fd647fe596..a57bf7904c 100644 --- a/bio/sourmash/compute/environment.yaml +++ b/bio/sourmash/compute/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - sourmash==2.0.0a7 diff --git a/bio/spades/metaspades/environment.yaml b/bio/spades/metaspades/environment.yaml index ecf97fe4ee..d2ecbfdc4b 100644 --- a/bio/spades/metaspades/environment.yaml +++ b/bio/spades/metaspades/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - spades >=3.15 - python >=3.5, <3.10 # spades doesn't support yet py 3.10 https://github.com/ablab/spades/issues/863 diff --git a/bio/sra-tools/fasterq-dump/environment.yaml b/bio/sra-tools/fasterq-dump/environment.yaml index 4327d0e2f5..fb9f7b8df7 100644 --- a/bio/sra-tools/fasterq-dump/environment.yaml +++ b/bio/sra-tools/fasterq-dump/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - sra-tools >2.9.1 - pigz >=2.6 diff --git a/bio/star/align/environment.yaml b/bio/star/align/environment.yaml index 0aacdc63e0..b7f7eef6f1 100644 --- a/bio/star/align/environment.yaml +++ b/bio/star/align/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - star =2.7 diff --git a/bio/star/index/environment.yaml b/bio/star/index/environment.yaml index 0aacdc63e0..b7f7eef6f1 100644 --- a/bio/star/index/environment.yaml +++ b/bio/star/index/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - star =2.7 diff --git a/bio/strelka/germline/environment.yaml b/bio/strelka/germline/environment.yaml index 664acacfe0..bfbee4b702 100644 --- a/bio/strelka/germline/environment.yaml +++ b/bio/strelka/germline/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strelka ==2.9.10 diff --git a/bio/strelka/somatic/environment.yaml b/bio/strelka/somatic/environment.yaml index 664acacfe0..bfbee4b702 100644 --- a/bio/strelka/somatic/environment.yaml +++ b/bio/strelka/somatic/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strelka ==2.9.10 diff --git a/bio/strling/call/environment.yaml b/bio/strling/call/environment.yaml index 30eec79ed2..121d7b4dbe 100644 --- a/bio/strling/call/environment.yaml +++ b/bio/strling/call/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strling ==0.3 diff --git a/bio/strling/extract/environment.yaml b/bio/strling/extract/environment.yaml index 30eec79ed2..121d7b4dbe 100644 --- a/bio/strling/extract/environment.yaml +++ b/bio/strling/extract/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strling ==0.3 diff --git a/bio/strling/index/environment.yaml b/bio/strling/index/environment.yaml index 30eec79ed2..121d7b4dbe 100644 --- a/bio/strling/index/environment.yaml +++ b/bio/strling/index/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strling ==0.3 diff --git a/bio/strling/merge/environment.yaml b/bio/strling/merge/environment.yaml index 30eec79ed2..121d7b4dbe 100644 --- a/bio/strling/merge/environment.yaml +++ b/bio/strling/merge/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - strling ==0.3 diff --git a/bio/subread/featurecounts/environment.yaml b/bio/subread/featurecounts/environment.yaml index 1277fee326..21e86fb9e0 100644 --- a/bio/subread/featurecounts/environment.yaml +++ b/bio/subread/featurecounts/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - subread =2.0 diff --git a/bio/tabix/environment.yaml b/bio/tabix/environment.yaml index e32a5017ab..97b1633916 100644 --- a/bio/tabix/environment.yaml +++ b/bio/tabix/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - htslib ==1.10 diff --git a/bio/tabix/query/environment.yaml b/bio/tabix/query/environment.yaml index c7437f87a8..64fa1205e1 100644 --- a/bio/tabix/query/environment.yaml +++ b/bio/tabix/query/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - htslib==1.12 diff --git a/bio/transdecoder/longorfs/environment.yaml b/bio/transdecoder/longorfs/environment.yaml index 491de42337..edcde2ecc6 100644 --- a/bio/transdecoder/longorfs/environment.yaml +++ b/bio/transdecoder/longorfs/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda - dependencies: + - defaults +dependencies: - transdecoder=5.5.0 diff --git a/bio/transdecoder/predict/environment.yaml b/bio/transdecoder/predict/environment.yaml index 12210013b8..c1eada02b3 100644 --- a/bio/transdecoder/predict/environment.yaml +++ b/bio/transdecoder/predict/environment.yaml @@ -1,5 +1,6 @@ channels: - conda-forge - bioconda - dependencies: + - defaults +dependencies: - transdecoder=5.5.0 diff --git a/bio/trim_galore/pe/environment.yaml b/bio/trim_galore/pe/environment.yaml index fabe131519..5d38f7df18 100644 --- a/bio/trim_galore/pe/environment.yaml +++ b/bio/trim_galore/pe/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - trim-galore ==0.6.6 diff --git a/bio/trim_galore/se/environment.yaml b/bio/trim_galore/se/environment.yaml index fabe131519..5d38f7df18 100644 --- a/bio/trim_galore/se/environment.yaml +++ b/bio/trim_galore/se/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - trim-galore ==0.6.6 diff --git a/bio/trimmomatic/pe/environment.yaml b/bio/trimmomatic/pe/environment.yaml index a20f65d4cd..eca75970ee 100644 --- a/bio/trimmomatic/pe/environment.yaml +++ b/bio/trimmomatic/pe/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - trimmomatic ==0.36 - pigz ==2.3.4 diff --git a/bio/trimmomatic/se/environment.yaml b/bio/trimmomatic/se/environment.yaml index a20f65d4cd..eca75970ee 100644 --- a/bio/trimmomatic/se/environment.yaml +++ b/bio/trimmomatic/se/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - trimmomatic ==0.36 - pigz ==2.3.4 diff --git a/bio/trinity/environment.yaml b/bio/trinity/environment.yaml index 4f087fa0d2..21813386d7 100644 --- a/bio/trinity/environment.yaml +++ b/bio/trinity/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - trinity ==2.8.4 diff --git a/bio/tximport/environment.yaml b/bio/tximport/environment.yaml index 900ab7fb1b..c5310a3ad3 100644 --- a/bio/tximport/environment.yaml +++ b/bio/tximport/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - bioconductor-tximport==1.14.0 - r-readr==1.3.1 diff --git a/bio/ucsc/bedGraphToBigWig/environment.yaml b/bio/ucsc/bedGraphToBigWig/environment.yaml index 752fead06f..2a558ffaab 100644 --- a/bio/ucsc/bedGraphToBigWig/environment.yaml +++ b/bio/ucsc/bedGraphToBigWig/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ucsc-bedgraphtobigwig == 377 \ No newline at end of file diff --git a/bio/ucsc/faToTwoBit/environment.yaml b/bio/ucsc/faToTwoBit/environment.yaml index b65a574d9a..d33bb854b2 100644 --- a/bio/ucsc/faToTwoBit/environment.yaml +++ b/bio/ucsc/faToTwoBit/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ucsc-fatotwobit == 377 \ No newline at end of file diff --git a/bio/ucsc/gtfToGenePred/environment.yaml b/bio/ucsc/gtfToGenePred/environment.yaml index c64a144631..0d7f49635b 100644 --- a/bio/ucsc/gtfToGenePred/environment.yaml +++ b/bio/ucsc/gtfToGenePred/environment.yaml @@ -1,6 +1,7 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ucsc-gtftogenepred =377 - csvkit =1.0 diff --git a/bio/ucsc/twoBitInfo/environment.yaml b/bio/ucsc/twoBitInfo/environment.yaml index 8e56eaabee..06b5cfae98 100644 --- a/bio/ucsc/twoBitInfo/environment.yaml +++ b/bio/ucsc/twoBitInfo/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ucsc-twobitinfo == 377 \ No newline at end of file diff --git a/bio/ucsc/twoBitToFa/environment.yaml b/bio/ucsc/twoBitToFa/environment.yaml index 554c8cc8fa..84460d3892 100644 --- a/bio/ucsc/twoBitToFa/environment.yaml +++ b/bio/ucsc/twoBitToFa/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - ucsc-twobittofa == 377 \ No newline at end of file diff --git a/bio/umis/bamtag/environment.yaml b/bio/umis/bamtag/environment.yaml index 5b1f26a27f..fbdca44317 100644 --- a/bio/umis/bamtag/environment.yaml +++ b/bio/umis/bamtag/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - umis ==1.0.3 - samtools ==1.9 diff --git a/bio/unicycler/environment.yaml b/bio/unicycler/environment.yaml index 11694d95bf..96b3025609 100644 --- a/bio/unicycler/environment.yaml +++ b/bio/unicycler/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - bowtie2 ==2.4.1 - bcftools ==1.10.2 diff --git a/bio/varscan/mpileup2indel/environment.yaml b/bio/varscan/mpileup2indel/environment.yaml index 61d79a29bb..b79d63dac5 100644 --- a/bio/varscan/mpileup2indel/environment.yaml +++ b/bio/varscan/mpileup2indel/environment.yaml @@ -1,7 +1,8 @@ name: varscan-pileup2indel channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - varscan ==2.4.3 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/varscan/mpileup2snp/environment.yaml b/bio/varscan/mpileup2snp/environment.yaml index 097e1bc4b8..3b326fad0d 100644 --- a/bio/varscan/mpileup2snp/environment.yaml +++ b/bio/varscan/mpileup2snp/environment.yaml @@ -1,7 +1,8 @@ name: varscan-pileup2snp channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - varscan ==2.4.3 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/varscan/somatic/environment.yaml b/bio/varscan/somatic/environment.yaml index 54cdd435cb..919105cff1 100644 --- a/bio/varscan/somatic/environment.yaml +++ b/bio/varscan/somatic/environment.yaml @@ -1,7 +1,8 @@ name: varscan channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - varscan ==2.4.3 - snakemake-wrapper-utils ==0.1.3 diff --git a/bio/vcftools/filter/environment.yaml b/bio/vcftools/filter/environment.yaml index deb0d57afe..ee7d29ff6b 100644 --- a/bio/vcftools/filter/environment.yaml +++ b/bio/vcftools/filter/environment.yaml @@ -1,5 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - vcftools ==0.1.16 diff --git a/bio/vembrane/filter/environment.yaml b/bio/vembrane/filter/environment.yaml index 63e7ea3366..dfb7a2686e 100644 --- a/bio/vembrane/filter/environment.yaml +++ b/bio/vembrane/filter/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge - default dependencies: - vembrane =0.5.1 diff --git a/bio/vembrane/table/environment.yaml b/bio/vembrane/table/environment.yaml index 63e7ea3366..dfb7a2686e 100644 --- a/bio/vembrane/table/environment.yaml +++ b/bio/vembrane/table/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge - default dependencies: - vembrane =0.5.1 diff --git a/bio/vep/annotate/environment.yaml b/bio/vep/annotate/environment.yaml index 78aeed004b..3bae5f5e21 100644 --- a/bio/vep/annotate/environment.yaml +++ b/bio/vep/annotate/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - ensembl-vep =105 - bcftools =1.12 diff --git a/bio/vep/cache/environment.yaml b/bio/vep/cache/environment.yaml index de18a758b0..6d73964709 100644 --- a/bio/vep/cache/environment.yaml +++ b/bio/vep/cache/environment.yaml @@ -1,6 +1,6 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: # This version should not be changed unless the vep_install command needs an # update or suddenly stops working. diff --git a/bio/vg/construct/environment.yaml b/bio/vg/construct/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/construct/environment.yaml +++ b/bio/vg/construct/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/ids/environment.yaml b/bio/vg/ids/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/ids/environment.yaml +++ b/bio/vg/ids/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/index/gcsa/environment.yaml b/bio/vg/index/gcsa/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/index/gcsa/environment.yaml +++ b/bio/vg/index/gcsa/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/index/xg/environment.yaml b/bio/vg/index/xg/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/index/xg/environment.yaml +++ b/bio/vg/index/xg/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/kmers/environment.yaml b/bio/vg/kmers/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/kmers/environment.yaml +++ b/bio/vg/kmers/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/merge/environment.yaml b/bio/vg/merge/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/merge/environment.yaml +++ b/bio/vg/merge/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/prune/environment.yaml b/bio/vg/prune/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/prune/environment.yaml +++ b/bio/vg/prune/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/vg/sim/environment.yaml b/bio/vg/sim/environment.yaml index 20f8fc610b..3e3e078e71 100644 --- a/bio/vg/sim/environment.yaml +++ b/bio/vg/sim/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - vg ==1.27.0 diff --git a/bio/wgsim/environment.yaml b/bio/wgsim/environment.yaml index c1e10bea6a..8f1cad8aac 100644 --- a/bio/wgsim/environment.yaml +++ b/bio/wgsim/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - defaults dependencies: - wgsim ==1.0.0 diff --git a/utils/cairosvg/environment.yaml b/utils/cairosvg/environment.yaml index 61ab8b1d29..8939b6944f 100644 --- a/utils/cairosvg/environment.yaml +++ b/utils/cairosvg/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - cairosvg =2.4.2 diff --git a/utils/nextflow/environment.yaml b/utils/nextflow/environment.yaml index 757fd6cab0..0934f828ff 100644 --- a/utils/nextflow/environment.yaml +++ b/utils/nextflow/environment.yaml @@ -1,5 +1,5 @@ channels: - - conda-forge - bioconda + - conda-forge dependencies: - nextflow