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commit 5ac1c9ce685f319d4c03d7e22a300d7c43c7d1f1 Author: Andreas Tille <[email protected]> Date: Sat Jul 25 08:12:20 2015 +0200 Rather maintain package in Git since the upstream tarball was changed --- debian/changelog | 22 ++++++++++++++++++++++ debian/compat | 1 + debian/control | 44 +++++++++++++++++++++++++++++++++++++++++++ debian/copyright | 25 ++++++++++++++++++++++++ debian/createmanpages | 16 ++++++++++++++++ debian/patches/makefile_patch | 26 +++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 31 ++++++++++++++++++++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 3 +++ 11 files changed, 182 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..7016687 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,22 @@ +ea-utils (1.1.2+dfsg-1) UNRELEASED; urgency=medium + + * Initial upload to Debian (Closes: #???) + + -- Andreas Tille <[email protected]> Sat, 25 Jul 2015 07:51:46 +0200 + +ea-utils (1.1.2-0biolinux4) trusty; urgency=medium + + * Re-remove utility copy of sparsehash as v2 is now in the + PPA. + * And don't forget to re-add the dependency + + -- Tim Booth <[email protected]> Thu, 22 Jan 2015 18:30:36 +0000 + +ea-utils (1.1.2-0biolinux2) trusty; urgency=low + + * Initial release for Bio-Linux 8 + * Build against samtools from Debian. + * Leave utility copy of sparsehash in for now, as Trusty + has v1 of the lib and we want v2. + + -- Tim Booth <[email protected]> Tue, 19 Aug 2014 16:19:00 +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..9dd2a89 --- /dev/null +++ b/debian/control @@ -0,0 +1,44 @@ +Source: ea-utils +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Tim Booth <[email protected]>, + Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + libbam-dev, + zlib1g-dev, + libgsl0-dev, + libsparsehash-dev (>= 2.0) +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/ +Homepage: https://code.google.com/p/ea-utils/ + +Package: ea-utils +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends}, + r-base-core +Description: Command-line tools for processing biological sequencing data + ...barcode demultiplexing, adapter trimming, etc. + . + Primarily written to support an Illumina based pipeline - but should work with + any FASTQs. + . + Main Tools are: + . + * fastq-mcf + Scans a sequence file for adapters, and, based on a log-scaled threshold, + determines a set of clipping parameters and performs clipping. Also does + skewing detection and quality filtering. + * fastq-multx + Demultiplexes a fastq. Capable of auto-determining barcode id's based on a + master set fields. Keeps multiple reads in-sync during demultiplexing. Can + verify that the reads are in-sync as well, and fail if they're not. + * fastq-join + Similar to audy's stitch program, but in C, more efficient and supports some + automatic benchmarking and tuning. It uses the same "squared distance for + anchored alignment" as other tools. + * varcall + Takes a pileup and calculates variants in a more easily parameterized manner + than some other tools. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..fc6aa30 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,25 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: ea-utils +Source: https://code.google.com/p/ea-utils/source/checkout +Files-Excluded: google + samtools + sparsehash + +Files: * +Copyright: © 2011 Erik Aronesty <[email protected]> + 2003-2006 Heng Li <[email protected]> + 2008 Jue Ruan <[email protected]> + Gunjan Hariani, + 2008-2009 Genome Research Ltd., + 2010 Illumina, Inc +License: MIT + +Files: debian/* +Copyright: © 2014 Tim Booth <[email protected]> + © 2015 Andreas Tille <[email protected]> +License: MIT + +TODO: + - use debian packaged samtools + - use debian packaged sparsehash + - some remaining files have BSD-3-clause diff --git a/debian/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..febcd91 --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,16 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +help2man --no-info --no-discard-stderr --help-option=" " \ + --name='<optional description of the program>' \ + --version-string="$VERSION" <programname> > $MANDIR/<programname>.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + diff --git a/debian/patches/makefile_patch b/debian/patches/makefile_patch new file mode 100644 index 0000000..abce167 --- /dev/null +++ b/debian/patches/makefile_patch @@ -0,0 +1,26 @@ +Author: Tim Booth <[email protected]> +Last-Update: Tue, 19 Aug 2014 16:19:00 +0100 +Description: Adapt Makefile to use Debian packaged libraries + +--- a/Makefile ++++ b/Makefile +@@ -77,12 +77,8 @@ + $(CC) $(CFLAGS) gcModel.c -o $@ $< + + # why the libbam.a doesn't work? not sure... *.o works +-sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h +-ifeq ($(OS),Windows_NT) +- $(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@ +-else +- $(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@ +-endif ++sam-stats: sam-stats.cpp fastq-lib.h ++ $(CC) $(CFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ + + samtools/libbam.a: samtools/*.c samtools/*.h + cd samtools && make libbam.a +@@ -102,4 +98,3 @@ + + clean: + rm -f *.o $(BIN) +- cd samtools && make clean diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..6a0d9f3 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +makefile_patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..88913a2 --- /dev/null +++ b/debian/rules @@ -0,0 +1,31 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# 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)) + +# To build with packages sparsehash change this to -I/usr/include/google +export CFLAGS:=$(CFLAGS) -I/usr/include/google +export CPPFLAGS:=$(CPPFLAGS) -I/usr/include/google + +%: + dh $@ + +override_dh_auto_install: + dh_auto_install -- PREFIX='$${DESTDIR}/usr' + +override_dh_auto_clean: + dh_auto_clean + +override_dh_clean: + dh_clean + #Kill convenience copies of code + rm -rf samtools + rm -rf google sparsehash 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..29dda79 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Cite-As: + Erik Aronesty (2011). ea-utils : "Command-line tools for processing biological sequencing data"; http://code.google.com/p/ea-utils +Reference: + Author: Erik Aronesty + Title: Comparison of Sequencing Utility Programs + Journal: The Open Bioinformatics Journal + Year: 2013 + Volume: 7 + Pages: 1-8 + DOI: 10.2174/1875036201307010001 + URL: http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1 + eprint: http://benthamopen.com/contents/pdf/TOBIOIJ/TOBIOIJ-7-1.pdf diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..e20aa30 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 + +# Upstream was linked via Google Drive, so there is no hope of a working watchfile. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ea-utils.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
