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Makefile.am
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ACLOCAL_AMFLAGS = -I m4
nodist_bin_SCRIPTS = \
pigx-rnaseq
dist_pkglibexec_SCRIPTS = \
snakefile.py \
qsub-template.sh
pkglibexec_scriptsdir = $(pkglibexecdir)/scripts
dist_pkglibexec_scripts_SCRIPTS = \
scripts/runDeseqReport.R \
scripts/translate_sample_sheet_for_report.R \
scripts/deseqReport.Rmd \
scripts/counts_matrix_from_SALMON.R \
scripts/validate_input.py \
scripts/norm_counts_deseq.R \
scripts/count_reads.R \
scripts/collate_read_counts.R \
scripts/collate_deseq_results.R \
scripts/validate_input_annotation.R
dist_pkgdata_DATA = \
etc/sample_sheet.csv.example \
etc/settings.yaml \
etc/pretty.txt \
images/Logo_PiGx.png
dist_doc_DATA = \
README.md
EXTRA_DIST = \
VERSION \
META.in \
tests/sample_sheet.csv \
tests/sample_data/sample.gtf \
tests/sample_data/reads/HBR_Rep1.read2.fastq.gz \
tests/sample_data/reads/HBR_Rep1.read1.fastq.gz \
tests/sample_data/reads/UHR_Rep1.read1.fastq.gz \
tests/sample_data/reads/UHR_Rep3.read1.fastq.gz \
tests/sample_data/reads/HBR_Rep2.read1.fastq.gz \
tests/sample_data/reads/UHR_Rep2.read1.fastq.gz \
tests/sample_data/reads/UHR_Rep2.read2.fastq.gz \
tests/sample_data/reads/HBR_Rep3.read2.fastq.gz \
tests/sample_data/reads/UHR_Rep1.read2.fastq.gz \
tests/sample_data/reads/HBR_Rep3.read1.fastq.gz \
tests/sample_data/reads/UHR_Rep3.read2.fastq.gz \
tests/sample_data/reads/HBR_Rep2.read2.fastq.gz \
tests/sample_data/sample.fasta \
tests/sample_data/sample.cdna.fasta \
tests/sample_data/preprocessed/colData.tsv \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/quant.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep1/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/quant.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep3/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/quant.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep2/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/quant.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep2/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/quant.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/UHR_Rep3/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/cmd_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/quant.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/quant.genes.sf \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/lib_format_counts.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/logs/salmon_quant.log \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/libParams/flenDist.txt \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/fld.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/expected_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/observed_bias.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/observed_bias_3p.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/obs5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/obs3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/exp5_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/exp3_seq.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/obs_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/exp_gc.gz \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/meta_info.json \
tests/sample_data/preprocessed/salmon_output/HBR_Rep1/aux_info/ambig_info.tsv \
tests/sample_data/preprocessed/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv \
tests/sample_data/preprocessed/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv \
tests/sample_data/preprocessed/feature_counts/raw_counts/hisat2/counts.tsv \
tests/sample_data/preprocessed/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv \
tests/sample_data/preprocessed/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv \
tests/sample_data/preprocessed/feature_counts/normalized/hisat2/deseq_size_factors.txt \
tests/sample_data/preprocessed/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep1.read_counts.csv \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep2.read_counts.csv \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep2.read_counts.csv \
tests/sample_data/preprocessed/mapped_reads/hisat2/UHR_Rep3.read_counts.csv \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep3.read_counts.csv \
tests/sample_data/preprocessed/mapped_reads/hisat2/HBR_Rep1.read_counts.csv \
tests/sample_data/preprocessed/trimmed_reads/HBR_Rep1.trimmed.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz \
tests/sample_data/preprocessed/trimmed_reads/UHR_Rep3.trimmed.fq.gz \
tests/settings.yaml \
tests/settings_no_de.yaml
AM_TESTS_ENVIRONMENT = srcdir="$(abs_top_srcdir)" builddir="$(abs_top_builddir)" PIGX_UNINSTALLED=1 PIGX_UGLY=1
TESTS = \
tests/test_genome_coverage/test.sh \
tests/test_deseq_reports/test.sh \
tests/test_multiqc/test.sh \
tests/test_hisat2_counts/test.sh \
tests/test_salmon_counts/test.sh \
tests/test_salmon/test_salmon_index.sh \
tests/test_salmon/test_salmon_quant.sh \
tests/test_hisat2/test.sh \
test.sh
clean-local:
-rm -rf .snakemake
-rm -rf tests/output
-rm -rf tests/output/.snakemake
-rm -rf tests/test_deseq_reports/config.json
-rm -rf tests/test_deseq_reports/logs
-rm -rf tests/test_deseq_reports/pigx_work
-rm -rf tests/test_deseq_reports/report
-rm -rf tests/test_deseq_reports/.snakemake
-rm -rf tests/test_deseq_reports/test.sh
-rm -rf tests/test_multiqc/config.json
-rm -rf tests/test_multiqc/logs
-rm -rf tests/test_multiqc/multiqc
-rm -rf tests/test_multiqc/pigx_work
-rm -rf tests/test_multiqc/.snakemake
-rm -rf tests/test_multiqc/test.sh
-rm -rf tests/test_salmon_counts/colData.tsv
-rm -rf tests/test_salmon_counts/logs/
-rm -rf tests/test_salmon_counts/pigx_work/
-rm -rf tests/test_salmon_counts/salmon_output/
-rm -rf tests/test_salmon_counts/.snakemake
-rm -rf tests/test_salmon_counts/test.sh
-rm -rf tests/test_salmon_counts/test.sh.log
-rm -rf tests/test_salmon_counts/test.sh.trs
-rm -rf tests/test_salmon/logs/
-rm -rf tests/test_salmon/pigx_work/
-rm -rf tests/test_salmon/salmon_index/
-rm -rf tests/test_salmon/salmon_output/
-rm -rf tests/test_salmon/.snakemake
-rm -rf tests/test_salmon/test_salmon_index.sh
-rm -rf tests/test_salmon/test_salmon_index.sh
-rm -rf tests/test_salmon/test_salmon_index.sh.log
-rm -rf tests/test_salmon/test_salmon_index.sh.trs
-rm -rf tests/test_salmon/test_salmon_quant.sh
-rm -rf tests/test_salmon/test_salmon_quant.sh
-rm -rf tests/test_salmon/test_salmon_quant.sh.log
-rm -rf tests/test_salmon/test_salmon_quant.sh.trs
-rm -rf tests/test_hisat2_counts/config.json
-rm -rf tests/test_hisat2_counts/pigx_work
-rm -rf tests/test_hisat2_counts/preprocessed_data
-rm -rf tests/test_hisat2_counts/.snakemake
-rm -rf tests/test_hisat2_counts/test.sh
-rm -rf tests/test_hisat2/Log.out
-rm -rf tests/test_hisat2/logs/
-rm -rf tests/test_hisat2/mapped_reads/
-rm -rf tests/test_hisat2/pigx_work/
-rm -rf tests/test_hisat2/.snakemake
-rm -rf tests/test_hisat2/star_index/
-rm -rf tests/test_hisat2/test.sh
-rm -rf tests/test_hisat2/test.sh.log
-rm -rf tests/test_hisat2/test.sh.trs
CLEANFILES = $(nodist_bin_SCRIPTS) config.json
# Build docker image with Guix
docker: dist
guix pack -C none -e '(load "guix.scm")' --with-source=pigx_rnaseq-$(VERSION).tar.gz -f docker -S /bin=bin -S /lib=lib -S /share=share glibc-utf8-locales tzdata coreutils bash