[med-svn] [trinityrnaseq] 03/03: skip DESeq2 test

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 2866f1be0c843288515a1aadbe993c73dc378ec9
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
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: ${shlibs:Depends},
          samtools,
          jellyfish,
          r-base-core,
+         r-cran-cluster,
          r-bioc-edger,
+         r-bioc-qvalue,
          rsem,
          berkeley-express,
          trimmomatic,
diff --git a/debian/patches/series b/debian/patches/series
index bb78d37..0466480 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
-skip-kallisto-tests
+skip-kallisto-deseq2-tests
 hashbang
 chrysalis-make-tweak
 noExitTester
diff --git a/debian/patches/skip-kallisto-deseq2-tests b/debian/patches/skip-kallisto-deseq2-tests
new file mode 100644
index 0000000..d22ce5f
--- /dev/null
+++ b/debian/patches/skip-kallisto-deseq2-tests
@@ -0,0 +1,57 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: skip tests for kallisto & DESeq2 programs; not currently pacakged for
+Debian
+--- trinityrnaseq.orig/sample_data/test_DE_analysis/Makefile
++++ trinityrnaseq/sample_data/test_DE_analysis/Makefile
+@@ -7,16 +7,21 @@
+ 	cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl  --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
+ 
+ test_DESeq2:
++ifeq "" "$(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 <crusoe at ucdavis.edu>
-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

-- 
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