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commit 2866f1be0c843288515a1aadbe993c73dc378ec9 Author: Michael R. Crusoe <[email protected]> Date: Fri Jan 15 08:12:18 2016 -0800 skip DESeq2 test --- debian/control | 2 ++ debian/patches/series | 2 +- debian/patches/skip-kallisto-deseq2-tests | 57 +++++++++++++++++++++++++++++++ debian/patches/skip-kallisto-tests | 17 --------- 4 files changed, 60 insertions(+), 18 deletions(-) diff --git a/debian/control b/debian/control index d0043db..5d5f354 100644 --- a/debian/control +++ b/debian/control @@ -34,7 +34,9 @@ Depends: ${shlibs:Depends}, samtools, jellyfish, r-base-core, + r-cran-cluster, r-bioc-edger, + r-bioc-qvalue, rsem, berkeley-express, trimmomatic, diff --git a/debian/patches/series b/debian/patches/series index bb78d37..0466480 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,4 @@ -skip-kallisto-tests +skip-kallisto-deseq2-tests hashbang chrysalis-make-tweak noExitTester diff --git a/debian/patches/skip-kallisto-deseq2-tests b/debian/patches/skip-kallisto-deseq2-tests new file mode 100644 index 0000000..d22ce5f --- /dev/null +++ b/debian/patches/skip-kallisto-deseq2-tests @@ -0,0 +1,57 @@ +Author: Michael R. Crusoe <[email protected]> +Description: skip tests for kallisto & DESeq2 programs; not currently pacakged for +Debian +--- trinityrnaseq.orig/sample_data/test_DE_analysis/Makefile ++++ trinityrnaseq/sample_data/test_DE_analysis/Makefile +@@ -7,16 +7,21 @@ + cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt + + test_DESeq2: ++ifeq "" "$(shell which DESeq2)" ++ echo skipping DESeq2 test ++else + ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir + cd DESeq2_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt ++endif + + test_voom: + ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir + cd voom_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt + + test_ROTS: +- ../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method ROTS -s samples.txt -o ROTS_outdir --ROTS_B 50 # make it go faster, use more in practice +- cd ROTS_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt ++ # disabled for now ++ #../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method ROTS -s samples.txt -o ROTS_outdir --ROTS_B 50 # make it go faster, use more in practice ++ #cd ROTS_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt + + clean: + rm -rf ./edgeR_outdir +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/Makefile ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/Makefile +@@ -24,7 +24,11 @@ + ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_PE + + test_kallisto: ++ifeq "" "$(shell which kallisto)" ++ echo skipping kallisto test ++else + ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --est_method kallisto --trinity_mode --prep_reference --output_dir kallisto_PE ++endif + + test_bowtie_PE_read_estimates: + ../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie +--- trinityrnaseq.orig/sample_data/test_align_and_estimate_abundance/Makefile ++++ trinityrnaseq/sample_data/test_align_and_estimate_abundance/Makefile +@@ -9,7 +9,11 @@ + ./align_and_estimate_tester.pl eXpress + + test_kallisto: ++ifeq "" "$(shell which kallisto)" ++ echo skipping kallisto test ++else + ./align_and_estimate_tester.pl kallisto ++endif + + + clean: diff --git a/debian/patches/skip-kallisto-tests b/debian/patches/skip-kallisto-tests deleted file mode 100644 index 58b7409..0000000 --- a/debian/patches/skip-kallisto-tests +++ /dev/null @@ -1,17 +0,0 @@ -Author: Michael R. Crusoe <[email protected]> -Description: skip tests for the kallisto program; not currently pacakged for -Debian ---- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/Makefile -+++ trinityrnaseq/sample_data/test_Trinity_Assembly/Makefile -@@ -24,7 +24,11 @@ - ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_PE - - test_kallisto: -+ifeq "" "$(shell which kallisto)" -+ echo skipping kallisto test -+else - ../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --est_method kallisto --trinity_mode --prep_reference --output_dir kallisto_PE -+endif - - test_bowtie_PE_read_estimates: - ../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
