Author: tille Date: 2015-07-25 05:42:59 +0000 (Sat, 25 Jul 2015) New Revision: 19705
Added: trunk/packages/ea-utils/ trunk/packages/ea-utils/trunk/ trunk/packages/ea-utils/trunk/debian/ trunk/packages/ea-utils/trunk/debian/changelog trunk/packages/ea-utils/trunk/debian/compat trunk/packages/ea-utils/trunk/debian/control trunk/packages/ea-utils/trunk/debian/copyright trunk/packages/ea-utils/trunk/debian/createmanpages trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git trunk/packages/ea-utils/trunk/debian/patches/ trunk/packages/ea-utils/trunk/debian/patches/makefile_patch trunk/packages/ea-utils/trunk/debian/patches/series trunk/packages/ea-utils/trunk/debian/rules trunk/packages/ea-utils/trunk/debian/source/ trunk/packages/ea-utils/trunk/debian/source/format trunk/packages/ea-utils/trunk/debian/upstream/ trunk/packages/ea-utils/trunk/debian/upstream/metadata trunk/packages/ea-utils/trunk/debian/watch Log: Inject further dependency of qiime as packaged by BioLinux Added: trunk/packages/ea-utils/trunk/debian/changelog =================================================================== --- trunk/packages/ea-utils/trunk/debian/changelog (rev 0) +++ trunk/packages/ea-utils/trunk/debian/changelog 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,16 @@ +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 Added: trunk/packages/ea-utils/trunk/debian/compat =================================================================== --- trunk/packages/ea-utils/trunk/debian/compat (rev 0) +++ trunk/packages/ea-utils/trunk/debian/compat 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1 @@ +9 Added: trunk/packages/ea-utils/trunk/debian/control =================================================================== --- trunk/packages/ea-utils/trunk/debian/control (rev 0) +++ trunk/packages/ea-utils/trunk/debian/control 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,38 @@ +Source: ea-utils +Section: science +Priority: optional +Maintainer: Tim Booth <[email protected]> +Uploaders: Debian Med Packaging Team <[email protected]> +Build-Depends: debhelper (>= 9), libbam-dev, zlib1g-dev, libgsl0-dev, + libsparsehash-dev (>= 2.0) +Standards-Version: 3.9.5 +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. Added: trunk/packages/ea-utils/trunk/debian/copyright =================================================================== --- trunk/packages/ea-utils/trunk/debian/copyright (rev 0) +++ trunk/packages/ea-utils/trunk/debian/copyright 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,16 @@ +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: * +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]> +License: MIT Added: trunk/packages/ea-utils/trunk/debian/createmanpages =================================================================== --- trunk/packages/ea-utils/trunk/debian/createmanpages (rev 0) +++ trunk/packages/ea-utils/trunk/debian/createmanpages 2015-07-25 05:42:59 UTC (rev 19705) @@ -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 + Property changes on: trunk/packages/ea-utils/trunk/debian/createmanpages ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git =================================================================== --- trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git (rev 0) +++ trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,18 @@ +#!/bin/sh -e + +echo "Please verify whether this script is obsoleted by gbp-create-remote-repo !" + +# This script implements the "Git tips" given here +# http://debian-med.alioth.debian.org/docs/policy.html#git-tips +# Use it with caution since it is less testet + +DEBPKGNAME=`dpkg-parsechangelog | awk '/^Source:/ {print $2}'` +SHORTDESC=`grep "^Description: " debian/control | head -n 1 | sed 's/^Description: //'` +VCSGIT=`grep "^Vcs-Git: " debian/control | sed -e 's/^Vcs-Git: //' -e 's#git://anonscm.debian.org/#ssh://git.debian.org/git/#'` +DIRatALIOTH=`echo $VCSGIT | sed -e 's#ssh://git.debian.org/git/#/git/#' -e 's#/[^/]\+\.git##'` + +ssh git.debian.org "cd $DIRatALIOTH; ./setup-repository $DEBPKGNAME '$SHORTDESC'" +git remote add origin $VCSGIT +git push origin master +git push --all --set-upstream +git push --tags Property changes on: trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/ea-utils/trunk/debian/patches/makefile_patch =================================================================== --- trunk/packages/ea-utils/trunk/debian/patches/makefile_patch (rev 0) +++ trunk/packages/ea-utils/trunk/debian/patches/makefile_patch 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,22 @@ +--- 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 Added: trunk/packages/ea-utils/trunk/debian/patches/series =================================================================== --- trunk/packages/ea-utils/trunk/debian/patches/series (rev 0) +++ trunk/packages/ea-utils/trunk/debian/patches/series 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1 @@ +makefile_patch Added: trunk/packages/ea-utils/trunk/debian/rules =================================================================== --- trunk/packages/ea-utils/trunk/debian/rules (rev 0) +++ trunk/packages/ea-utils/trunk/debian/rules 2015-07-25 05:42:59 UTC (rev 19705) @@ -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=-I. +export CPPFLAGS=-I. + +%: + 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 Property changes on: trunk/packages/ea-utils/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/ea-utils/trunk/debian/source/format =================================================================== --- trunk/packages/ea-utils/trunk/debian/source/format (rev 0) +++ trunk/packages/ea-utils/trunk/debian/source/format 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/ea-utils/trunk/debian/upstream/metadata =================================================================== --- trunk/packages/ea-utils/trunk/debian/upstream/metadata (rev 0) +++ trunk/packages/ea-utils/trunk/debian/upstream/metadata 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,12 @@ +Reference: + Author: Erik Aronesty + Title: Comparison of Sequencing Utility Programs + Journal: The Open Bioinformatics Journal + Year:2013 + Volume: + Number: + Pages:8 + DOI: 10.2174/1875036201307010001 + PMID: + URL: http://benthamopen.com/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm + eprint: Added: trunk/packages/ea-utils/trunk/debian/watch =================================================================== --- trunk/packages/ea-utils/trunk/debian/watch (rev 0) +++ trunk/packages/ea-utils/trunk/debian/watch 2015-07-25 05:42:59 UTC (rev 19705) @@ -0,0 +1,3 @@ +version=3 + +# Upstream was linked via Google Drive, so there is no hope of a working watchfile. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
