This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository sparta.
commit 66de60cb60ab8113ce0f275b36b0ae025f5881be Author: Andreas Tille <[email protected]> Date: Wed Aug 3 11:36:27 2016 +0200 Versioned Build-Depends: python-htseq (>= 0.6.1p1) --- debian/control | 2 +- debian/patches/fix_htseq_call.patch | 28 ++++++++++++++++++++++++++++ 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 5b8e90b..6f6ab65 100644 --- a/debian/control +++ b/debian/control @@ -22,7 +22,7 @@ Depends: ${python:Depends}, fastqc, trimmomatic, bowtie, - python-htseq + python-htseq (>= 0.6.1p1) Description: automated reference-based bacterial RNA-seq Transcriptome Analysis SPARTA is a workflow aimed at analyzing single-end Illumina RNA-seq data. The workflow combines several tools: Trimmomatic (read diff --git a/debian/patches/fix_htseq_call.patch b/debian/patches/fix_htseq_call.patch new file mode 100644 index 0000000..934c0b5 --- /dev/null +++ b/debian/patches/fix_htseq_call.patch @@ -0,0 +1,28 @@ +Author: Andreas Tille <[email protected]> +Last-Updata: Thu, 28 Jul 2016 15:13:14 +0200 +Description: Deactivated, wanted to see the htseq-count call and learned + that a versioned Build-Depends python-htseq (>= 0.6.1p1) is needed + +--- a/mapping_and_counting.py ++++ b/mapping_and_counting.py +@@ -86,12 +86,16 @@ class Mapping_and_Counting(object): + fname = os.path.splitext(mapfile)[0] + strippedmapfile = fname[len('align'):] + if options.verbose: +- subprocess.Popen("./htseq-count --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam"), shell=True).wait() ++ htsc = "htseq-count" + else: +- subprocess.Popen("./htseq-count --quiet --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam"), shell=True).wait() ++ htsc = "htseq-count --quiet" ++ ++ htseqcall= htsc + " --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam") ++ print "DEBUG:", htseqcall ++ subprocess.Popen(htseqcall, shell=True).wait() + + if options.cleanup: + for file in os.listdir(os.path.join(analysislocation, "Bowtie")): + subprocess.Popen("rm " + os.path.join(analysislocation, "Bowtie", "{file}".format(file=file)), shell=True).wait() + +- return +\ No newline at end of file ++ return -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sparta.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
