[med-svn] r21313 - in trunk/packages: . ngopt ngopt/trunk ngopt/trunk/debian ngopt/trunk/debian/bin ngopt/trunk/debian/source ngopt/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Wed Jan 27 18:41:14 UTC 2016
Author: tille
Date: 2016-01-27 18:41:13 +0000 (Wed, 27 Jan 2016)
New Revision: 21313
Added:
trunk/packages/ngopt/
trunk/packages/ngopt/trunk/
trunk/packages/ngopt/trunk/debian/
trunk/packages/ngopt/trunk/debian/README.source
trunk/packages/ngopt/trunk/debian/bin/
trunk/packages/ngopt/trunk/debian/bin/a5_pipeline
trunk/packages/ngopt/trunk/debian/bin/test.a5.sh
trunk/packages/ngopt/trunk/debian/changelog
trunk/packages/ngopt/trunk/debian/compat
trunk/packages/ngopt/trunk/debian/control
trunk/packages/ngopt/trunk/debian/copyright
trunk/packages/ngopt/trunk/debian/docs
trunk/packages/ngopt/trunk/debian/examples
trunk/packages/ngopt/trunk/debian/install
trunk/packages/ngopt/trunk/debian/rules
trunk/packages/ngopt/trunk/debian/source/
trunk/packages/ngopt/trunk/debian/source/format
trunk/packages/ngopt/trunk/debian/upstream/
trunk/packages/ngopt/trunk/debian/upstream/metadata
trunk/packages/ngopt/trunk/debian/watch
Log:
Inject ngopt (no intend to upload this non-policy conform packaging attempt)
Added: trunk/packages/ngopt/trunk/debian/README.source
===================================================================
--- trunk/packages/ngopt/trunk/debian/README.source (rev 0)
+++ trunk/packages/ngopt/trunk/debian/README.source 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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
Added: trunk/packages/ngopt/trunk/debian/bin/a5_pipeline
===================================================================
--- trunk/packages/ngopt/trunk/debian/bin/a5_pipeline (rev 0)
+++ trunk/packages/ngopt/trunk/debian/bin/a5_pipeline 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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 $@
Property changes on: trunk/packages/ngopt/trunk/debian/bin/a5_pipeline
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/ngopt/trunk/debian/bin/test.a5.sh
===================================================================
--- trunk/packages/ngopt/trunk/debian/bin/test.a5.sh (rev 0)
+++ trunk/packages/ngopt/trunk/debian/bin/test.a5.sh 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+pkg=ngopt
+
+if [ "$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
Property changes on: trunk/packages/ngopt/trunk/debian/bin/test.a5.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/ngopt/trunk/debian/changelog
===================================================================
--- trunk/packages/ngopt/trunk/debian/changelog (rev 0)
+++ trunk/packages/ngopt/trunk/debian/changelog 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1,5 @@
+ngopt (0.0.20150522-1) local; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Wed, 27 Jan 2016 15:33:44 +0100
Added: trunk/packages/ngopt/trunk/debian/compat
===================================================================
--- trunk/packages/ngopt/trunk/debian/compat (rev 0)
+++ trunk/packages/ngopt/trunk/debian/compat 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1 @@
+9
Added: trunk/packages/ngopt/trunk/debian/control
===================================================================
--- trunk/packages/ngopt/trunk/debian/control (rev 0)
+++ trunk/packages/ngopt/trunk/debian/control 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ngopt/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ngopt/trunk/
+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
Added: trunk/packages/ngopt/trunk/debian/copyright
===================================================================
--- trunk/packages/ngopt/trunk/debian/copyright (rev 0)
+++ trunk/packages/ngopt/trunk/debian/copyright 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2014 maintainername <maintainer at e.mail>
+License: <license>
Added: trunk/packages/ngopt/trunk/debian/docs
===================================================================
--- trunk/packages/ngopt/trunk/debian/docs (rev 0)
+++ trunk/packages/ngopt/trunk/debian/docs 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1,2 @@
+README.txt
+debian/bin/test.a5.sh
Added: trunk/packages/ngopt/trunk/debian/examples
===================================================================
--- trunk/packages/ngopt/trunk/debian/examples (rev 0)
+++ trunk/packages/ngopt/trunk/debian/examples 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1 @@
+example/*
Added: trunk/packages/ngopt/trunk/debian/install
===================================================================
--- trunk/packages/ngopt/trunk/debian/install (rev 0)
+++ trunk/packages/ngopt/trunk/debian/install 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1,3 @@
+debian/bin/a5* usr/bin
+bin usr/lib/a5
+adapter.fasta usr/lib/a5
Added: trunk/packages/ngopt/trunk/debian/rules
===================================================================
--- trunk/packages/ngopt/trunk/debian/rules (rev 0)
+++ trunk/packages/ngopt/trunk/debian/rules 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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
Property changes on: trunk/packages/ngopt/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/ngopt/trunk/debian/source/format
===================================================================
--- trunk/packages/ngopt/trunk/debian/source/format (rev 0)
+++ trunk/packages/ngopt/trunk/debian/source/format 2016-01-27 18:41:13 UTC (rev 21313)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/ngopt/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/ngopt/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/ngopt/trunk/debian/upstream/metadata 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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
Added: trunk/packages/ngopt/trunk/debian/watch
===================================================================
--- trunk/packages/ngopt/trunk/debian/watch (rev 0)
+++ trunk/packages/ngopt/trunk/debian/watch 2016-01-27 18:41:13 UTC (rev 21313)
@@ -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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