[med-svn] [trinityrnaseq] 01/03: skip the kallisto test

[Michael Crusoe]

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

commit acdf873c8d083d69f59cd1e311c3d47c2d8977ab
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 06:02:01 2016 -0800

    skip the kallisto test
---
 debian/patches/series              |  1 +
 debian/patches/skip-kallisto-tests | 17 +++++++++++++++++
 2 files changed, 18 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index ab49bc3..dcd2222 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+skip-kallisto-tests
 hashbang
 chrysalis-make-tweak
 noExitTester
diff --git a/debian/patches/skip-kallisto-tests b/debian/patches/skip-kallisto-tests
new file mode 100644
index 0000000..58b7409
--- /dev/null
+++ b/debian/patches/skip-kallisto-tests
@@ -0,0 +1,17 @@
+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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