[med-svn] [seqsero] 02/02: Add initial Debian packaging
Andreas Tille
tille at debian.org
Fri Feb 17 14:57:54 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqsero.
commit 654a94b6ccc6ce16f7ec5f8ce4b16094561a8fc4
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 17 15:51:24 2017 +0100
Add initial Debian packaging
---
debian/changelog | 12 +++++++
debian/compat | 1 +
debian/control | 40 ++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++
debian/docs | 2 ++
debian/get-orig-source | 55 +++++++++++++++++++++++++++++++
debian/install | 4 +++
debian/links | 1 +
debian/patches/fix_perl_interpreter.patch | 19 +++++++++++
debian/patches/series | 1 +
debian/rules | 30 +++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++
debian/watch | 4 +++
14 files changed, 210 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ca8214b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,12 @@
+seqsero (1.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+ TODO:
+ - See whether upstream will add release tags
+ https://github.com/denglab/SeqSero/issues/2
+ otherwise fix get-orig-source
+ - Find source code of isPcr33. Seems to be connected with
+ https://github.com/ENCODE-DCC/kentUtils.git
+
+ -- Andreas Tille <tille at debian.org> Wed, 15 Feb 2017 09:17:30 +0100
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..c9be3fe
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,40 @@
+Source: seqsero
+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 (>= 10),
+ dh-python,
+ python
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/seqsero.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/seqsero.git
+Homepage: https://github.com/denglab/SeqSero
+
+Package: seqsero
+Architecture: all
+Depends: ${python:Depends},
+ ${misc:Depends},
+ python-biopython,
+ bwa,
+ samtools,
+ sra-toolkit
+Description: Salmonella serotyping from genome sequencing data
+ SeqSero is a pipeline for Salmonella serotype determination from raw
+ sequencing reads or genome assemblies.
+ .
+ SeqSero is a novel tool for determining Salmonella serotypes using high-
+ throughput genome sequencing data. SeqSero is based on curated databases
+ of Salmonella serotype determinants (rfb gene cluster, fliC and fljB
+ alleles) and is predicted to determine serotype rapidly and accurately
+ for nearly the full spectrum of Salmonella serotypes (more than 2,300
+ serotypes), from both raw sequencing reads and genome assemblies. The
+ performance of SeqSero was evaluated by testing
+ 1. raw reads from genomes of 308 Salmonella isolates of known serotype
+ 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and
+ made publicly available by GenomeTrakr, a U.S. national monitoring
+ network operated by the Food and Drug Administration; and
+ 3. 354 other publicly available draft or complete Salmonella genomes.
+ SeqSero can help to maintain the well-established utility of Salmonella
+ serotyping when integrated into a platform of WGS-based pathogen
+ subtyping and characterization.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..233cfd8
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SeqSero
+Upstream-Contact: seqsero at gmail.com
+Source: https://github.com/denglab/SeqSero
+Files-Excluded: libs/isPcr
+ */*.pyc
+
+Files: *
+Copyright: 2014-2015 University of Georgia
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find a full copy of the GNU General Public
+ License at /usr/share/common-licenses/GPL-2.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..5554c61
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.md
+User_manual.pdf
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..2aa782f
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,55 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+# Excluding files and repacking archives
+# --------------------------------------
+# See also mk-origtargz(1) and the --repack option to uscan(1), which
+# honor the Files-Excluded list in debian/copyright.
+# That may be all you need, especially since the repack option can be set
+# in debian/watch.
+
+# For an example how to fetch source from sourceforge SVN see
+# https://anonscm.debian.org/git/debian-med/kmer-tools.git
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+tar -xaf ../${TARDIR}.tar.gz
+
+UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
+if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
+ mv "${UPSTREAMTARDIR}" "${TARDIR}"
+fi
+
+# Remove useless binaries
+# ... do something which needs to be done ...
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..775db38
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+database usr/share/seqsero
+libs usr/share/seqsero
+primers usr/share/seqsero
+SeqSero.py usr/share/seqsero
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..db069d2
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/share/seqsero/SeqSero.py usr/bin/seqsero
diff --git a/debian/patches/fix_perl_interpreter.patch b/debian/patches/fix_perl_interpreter.patch
new file mode 100644
index 0000000..e2bc2aa
--- /dev/null
+++ b/debian/patches/fix_perl_interpreter.patch
@@ -0,0 +1,19 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 15 Feb 2017 09:17:30 +0100
+Description: Fix shebang line
+
+--- a/libs/split_interleaved_fastq.pl
++++ b/libs/split_interleaved_fastq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl-w
++#!/usr/bin/perl -w
+
+ use strict;
+
+@@ -314,4 +314,4 @@ Ram vinay pandey
+
+ =cut
+
+-
+\ No newline at end of file
++
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..471416f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_perl_interpreter.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..def9a27
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --with python2
+
+override_dh_fixperms:
+ dh_fixperms
+ find debian -name split_interleaved_fastq.pl -exec chmod +x \{\} \;
+
+#get-orig-source:
+# . debian/get-orig-source
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..89c3246
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Shaokang Zhang and Yanlong Yin and Marcus B. Jones and Zhenzhen Zhang and Brooke L. Deatherage Kaiser and Blake A. Dinsmore and Collette Fitzgerald and Patricia I. Fields and Xiangyu Deng
+ Title: "Salmonella Serotype Determination Utilizing High-throughput Genome Sequencing Data"
+ Journal: Journal of Clinical Microbiology
+ Year: 2015
+ Volume: 53
+ Number: 5
+ Pages: 1685-92
+ DOI: 10.1128/JCM.00323-15
+ PMID: 25762776
+ URL: http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15
+ eprint: http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..bafbd49
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/denglab/SeqSero/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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