[med-svn] [ngopt] 01/02: Add some packaging for ngopt that id currently only intended for local use
Andreas Tille
tille at debian.org
Thu Jan 28 09:10:33 UTC 2016
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tille pushed a commit to branch master
in repository ngopt.
commit 5e5794ab9f030dafb35c74acc6eb0890000f8d26
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org> 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <tille at debian.org>
+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)))
--
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