This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository ngopt.
commit 5e5794ab9f030dafb35c74acc6eb0890000f8d26 Author: Andreas Tille <[email protected]> Date: Thu Jan 28 10:05:47 2016 +0100 Add some packaging for ngopt that id currently only intended for local use --- debian/README.source | 22 ++++++++++++++++++++++ debian/bin/a5_pipeline | 9 +++++++++ debian/bin/test.a5.sh | 39 +++++++++++++++++++++++++++++++++++++++ debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 19 +++++++++++++++++++ debian/copyright | 23 +++++++++++++++++++++++ debian/docs | 2 ++ debian/examples | 1 + debian/install | 3 +++ debian/rules | 12 ++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 3 +++ 14 files changed, 152 insertions(+) diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..f7d01a0 --- /dev/null +++ b/debian/README.source @@ -0,0 +1,22 @@ +ngopt a5 pipeline +================= + +This Debian package is not properly built from source but rather throws +binary files from upstream download right into the file system. Thus +for the moment this is no target for a proper Debian release and rather +serves its purpose for a local installation. + +It should be possible to replace parts like + + * bwa + * idba + * sga + * samtools + * trimmomatic + * SSPACE (including bowtie) + +by the according Debian packages. Unfortunately the test suite leads +to different results when doing so (at least when starting with Debian +packaged bwa). So testing this needs some further investigation. + + -- Andreas Tille <[email protected]> Wed, 27 Jan 2016 15:33:44 +0100 \ No newline at end of file diff --git a/debian/bin/a5_pipeline b/debian/bin/a5_pipeline new file mode 100755 index 0000000..459fbb3 --- /dev/null +++ b/debian/bin/a5_pipeline @@ -0,0 +1,9 @@ +#!/bin/sh +CHECKDIRS="/usr/lib/a5/bin /usr/local/lib/a5 ${HOME}/usr/lib/a5" +for A5DIR in $CHECKDIRS ; do + if [ -d $A5DIR ] ; then break ; fi +done +echo $A5DIR +export PATH=$A5DIR:$PATH +set -x +$A5DIR/a5_pipeline.pl $@ diff --git a/debian/bin/test.a5.sh b/debian/bin/test.a5.sh new file mode 100755 index 0000000..b7529a7 --- /dev/null +++ b/debian/bin/test.a5.sh @@ -0,0 +1,39 @@ +#!/bin/bash + +pkg=ngopt + +if [ "$DIR" = "" ] ; then + DIR=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $DIR +cp -a /usr/share/doc/$pkg/examples $DIR/example +find . -name "*.gz" -exec gunzip \{\} \; + +base="test.phiX.a5" +echo "[test_a5] a5_pipeline --end=5 $DIR/example/phiX_p1.fastq $DIR/example/phiX_p2.fastq $base" +a5_pipeline --end=5 $DIR/example/phiX_p1.fastq $DIR/example/phiX_p2.fastq $base > $base.out 2> $base.err + +if [ ! -s $base.contigs.fasta ] ; then + echo "Test run of A5 unsuccessful. No contigs produced." + exit +elif [ ! -s $base.final.scaffolds.fasta ] ; then + echo "Test run of A5 unsuccessful. No scaffolds produced." + exit +else + echo "A5 successfully produced contigs and scaffolds." +fi + +NCHAR_REF=`cat $DIR/example/phiX.a5.final.scaffolds.fasta | wc -c | sed -e 's/\ //g'` +NCHAR_FINAL=`cat test.phiX.a5.final.scaffolds.fasta | wc -c | sed -e 's/\ //g'` + +NCHAR_DIFF=`expr $NCHAR_REF - $NCHAR_FINAL` +if [ $NCHAR_DIFF -lt 0 ]; then + NCHAR_DIFF=`expr $NCHAR_FINAL - $NCHAR_REF` +fi + +if [ $NCHAR_DIFF -gt 100 ]; then + echo "Test run of A5 unsuccessful." +else + echo "Test run of A5 successful. Removing temporary files." + rm -rf $base.* +fi diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..d475b5f --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +ngopt (0.0.20150522-1) local; urgency=low + + * local use, no intend to release + + -- Andreas Tille <[email protected]> Wed, 27 Jan 2016 15:33:44 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..ed1d343 --- /dev/null +++ b/debian/control @@ -0,0 +1,19 @@ +Source: ngopt +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.6 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ngopt.git +Vcs-Git: git://anonscm.debian.org/debian-med/ngopt.git +Homepage: http://sourceforge.net/projects/ngopt/ + +Package: ngopt +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: de novo assembly & analysis of Illumina sequence data + de novo assembly & analysis of Illumina sequence data, including the A5 + pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to + facilitate data submission to NCBI and the RAST annotation system diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..29dcb17 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,23 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: http://sourceforge.net/projects/ngopt/files/ + +Files: * +Copyright: 2011-2014 Andrew Tritt and Aaron Darling +License: GPL-3 +Comment: + A5-miseq is free, open source software licensed under the GPLv3, please + see the file LICENSE for details. The A5-miseq pipeline includes + open-source components developed and copyright by 3rd parties: `bwa`, + `samtools`, `SGA`, `bowtie`, `IDBA-UD`, `SSPACE`, and `Trimmomatic`. + . + Currently there is no intend to release this package. At first + it needs to be clarified how well it works with Debian packaged versions + of the said tools. + +Files: debian/* +Copyright: 2016 Andreas Tille <[email protected]> +License: GPL-3 + +License: GPL-3 + The full text of GPL version 3 can be found at + /usr/share/common-licenses/GPL-3. diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..0b73e32 --- /dev/null +++ b/debian/docs @@ -0,0 +1,2 @@ +README.txt +debian/bin/test.a5.sh diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..0bbe99e --- /dev/null +++ b/debian/examples @@ -0,0 +1 @@ +example/* diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..14db7f1 --- /dev/null +++ b/debian/install @@ -0,0 +1,3 @@ +debian/bin/a5* usr/bin +bin usr/lib/a5 +adapter.fasta usr/lib/a5 diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..2482fc9 --- /dev/null +++ b/debian/rules @@ -0,0 +1,12 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') + +%: + dh $@ + +#override_dh_installdocs: +# dh_installdocs +# sed 's?^$DIR/bin/a5_pipeline.pl?a5_pipeline?' test.a5.sh > debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/test.a5.sh diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..24743a2 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Andrew Tritt and Jonathan A. Eisen and Marc T. Facciotti and Aaron E. Darling + Title: "An Integrated Pipeline for de Novo Assembly of Microbial Genomes" + Journal: PLOSone + Year: 2012 + Volume: 7 + Number: 9 + Pages: e42304 + DOI: 10.1371/journal.pone.0042304 + PMID: 23028432 + URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042304 + eprint: http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0042304.PDF diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..4074d92 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=uversionmangle=s/^/0.0./ \ + http://sf.net/ngopt/a5_miseq_linux_(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ngopt.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
