This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository trinityrnaseq.
commit acdf873c8d083d69f59cd1e311c3d47c2d8977ab Author: Michael R. Crusoe <[email protected]> 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 <[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
