From f9c1cc772a8e8503dc659c1ed4a085e8e59f38cf Mon Sep 17 00:00:00 2001 From: Rob Chekaluk Date: Wed, 1 Nov 2023 08:15:33 -0400 Subject: [PATCH] Update mirbase.org URLs fixes https://github.com/bcbio/bcbio-nextgen/issues/3721 fixes https://github.com/bcbio/bcbio-nextgen/issues/3722 --- ggd-recipes/BDGP6/mirbase.yaml | 2 +- ggd-recipes/canFam3/mirbase.yaml | 4 ++-- ggd-recipes/hg19/mirbase.yaml | 2 +- ggd-recipes/hg38-noalt/mirbase.yaml | 4 ++-- ggd-recipes/hg38/mirbase.yaml | 4 ++-- ggd-recipes/mm10/mirbase.yaml | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/ggd-recipes/BDGP6/mirbase.yaml b/ggd-recipes/BDGP6/mirbase.yaml index 8806f5af4..21b8e91f3 100644 --- a/ggd-recipes/BDGP6/mirbase.yaml +++ b/ggd-recipes/BDGP6/mirbase.yaml @@ -19,7 +19,7 @@ recipe: cat mature.t.fa | awk '{if ($0~/>dme/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -nv -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/22/miRNA.str.gz && gunzip -f miRNA.t.str.gz cat miRNA.t.str | awk '{if ($0~/dme/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/22/genomes/dme.gff3 + wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/dme.gff3 wget --no-check-certificate -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip -f Rfam_for_miRDeep.fa.gz # targetscan analysis wget --random-wait --retry-connrefused --no-check-certificate -nv -c -O Summary_Counts.txt.zip http://www.targetscan.org/fly_72/fly_72_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip diff --git a/ggd-recipes/canFam3/mirbase.yaml b/ggd-recipes/canFam3/mirbase.yaml index bfbd1222f..0d9b16bfa 100644 --- a/ggd-recipes/canFam3/mirbase.yaml +++ b/ggd-recipes/canFam3/mirbase.yaml @@ -10,7 +10,7 @@ recipe: - | mkdir -p srnaseq cd srnaseq - wget --random-wait --retry-connrefused -q -c -O cfa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3 + wget --random-wait --retry-connrefused -q -c -O cfa.gff3 https://mirbase.org/download/cfa.gff3 awk '$3=="miRNA"' cfa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf wget --random-wait --retry-connrefused -q -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/rmsk.txt.gz zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf @@ -23,7 +23,7 @@ recipe: zcat mature.fa.gz | awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz zcat miRNA.str.gz | awk '{if ($0~/cfa/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3 + wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/cfa.gff3 # mintmap # mirdeep2 wget --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz diff --git a/ggd-recipes/hg19/mirbase.yaml b/ggd-recipes/hg19/mirbase.yaml index 4874c02c1..3ad2769d6 100644 --- a/ggd-recipes/hg19/mirbase.yaml +++ b/ggd-recipes/hg19/mirbase.yaml @@ -29,7 +29,7 @@ recipe: zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -nv -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3 + wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3 # tdrmapper wget --random-wait --retry-connrefused --no-check-certificate -nv -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa # mintmap diff --git a/ggd-recipes/hg38-noalt/mirbase.yaml b/ggd-recipes/hg38-noalt/mirbase.yaml index 2610e90f2..9088b4bd4 100644 --- a/ggd-recipes/hg38-noalt/mirbase.yaml +++ b/ggd-recipes/hg38-noalt/mirbase.yaml @@ -10,7 +10,7 @@ recipe: - | mkdir -p srnaseq cd srnaseq - wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3 + wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://mirbase.org/download/hsa.gff3 awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf wget --random-wait --retry-connrefused -q -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf @@ -30,7 +30,7 @@ recipe: zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3 + wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3 #tdrmapper wget --random-wait --retry-connrefused --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa # mintmap diff --git a/ggd-recipes/hg38/mirbase.yaml b/ggd-recipes/hg38/mirbase.yaml index 2610e90f2..9088b4bd4 100644 --- a/ggd-recipes/hg38/mirbase.yaml +++ b/ggd-recipes/hg38/mirbase.yaml @@ -10,7 +10,7 @@ recipe: - | mkdir -p srnaseq cd srnaseq - wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3 + wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://mirbase.org/download/hsa.gff3 awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf wget --random-wait --retry-connrefused -q -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf @@ -30,7 +30,7 @@ recipe: zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3 + wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3 #tdrmapper wget --random-wait --retry-connrefused --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa # mintmap diff --git a/ggd-recipes/mm10/mirbase.yaml b/ggd-recipes/mm10/mirbase.yaml index 850091a11..37b46f34a 100644 --- a/ggd-recipes/mm10/mirbase.yaml +++ b/ggd-recipes/mm10/mirbase.yaml @@ -24,7 +24,7 @@ recipe: zcat mature.fa.gz | awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz zcat miRNA.str.gz | awk '{if ($0~/mmu/)print $0}' > miRNA.str - wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/mmu.gff3 + wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/mmu.gff3 wget --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz # targetscan analysis # wget --no-check-certificate -q -c -O Summary_Counts.txt.zip http://www.targetscan.org/mmu_71/mmu_71_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip