Author: moeller Date: 2012-04-24 23:04:16 +0000 (Tue, 24 Apr 2012) New Revision: 10572
Added: trunk/packages/babraham/ trunk/packages/babraham/fastqc/ trunk/packages/babraham/fastqc/debian/ trunk/packages/babraham/fastqc/debian/README.Debian trunk/packages/babraham/fastqc/debian/README.source trunk/packages/babraham/fastqc/debian/changelog trunk/packages/babraham/fastqc/debian/compat trunk/packages/babraham/fastqc/debian/control trunk/packages/babraham/fastqc/debian/copyright trunk/packages/babraham/fastqc/debian/docs trunk/packages/babraham/fastqc/debian/menu trunk/packages/babraham/fastqc/debian/patches/ trunk/packages/babraham/fastqc/debian/patches/Makefile.patch trunk/packages/babraham/fastqc/debian/patches/fastqc.patch trunk/packages/babraham/fastqc/debian/patches/series trunk/packages/babraham/fastqc/debian/rules trunk/packages/babraham/fastqc/debian/source/ trunk/packages/babraham/fastqc/debian/source/format trunk/packages/babraham/fastqc/debian/watch.ex Log: ITP and debian/upstream coming. :o) The vast amoutn of NGS tools is truly amazing. The Babraham research institute has a nubmer of interesting such on their projects page. I am sufficiently confident that there is more to come, so I added that subdirectory. Added: trunk/packages/babraham/fastqc/debian/README.Debian =================================================================== --- trunk/packages/babraham/fastqc/debian/README.Debian (rev 0) +++ trunk/packages/babraham/fastqc/debian/README.Debian 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,7 @@ +fastqc for Debian +----------------- + +This package needs some testing and a man page. Help is appreciated, +especially with a debian/watch file. + + -- Steffen Moeller <[email protected]> Tue, 24 Apr 2012 20:05:34 +0200 Added: trunk/packages/babraham/fastqc/debian/README.source =================================================================== --- trunk/packages/babraham/fastqc/debian/README.source (rev 0) +++ trunk/packages/babraham/fastqc/debian/README.source 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,10 @@ +fastqc for Debian +----------------- + +The following .jar files were removed and are substituted with symbolic links to the .jars in the distribution. + +fastqc-0.10.0/jbzip2-0.9.jar +fastqc-0.10.0/sam-1.32.jar + +All .svn directories were removed from the source tree. + Added: trunk/packages/babraham/fastqc/debian/changelog =================================================================== --- trunk/packages/babraham/fastqc/debian/changelog (rev 0) +++ trunk/packages/babraham/fastqc/debian/changelog 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,5 @@ +fastqc (0.10.0-1) unstable; urgency=low + + * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + + -- Steffen Moeller <[email protected]> Tue, 24 Apr 2012 20:05:34 +0200 Added: trunk/packages/babraham/fastqc/debian/compat =================================================================== --- trunk/packages/babraham/fastqc/debian/compat (rev 0) +++ trunk/packages/babraham/fastqc/debian/compat 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1 @@ +8 Added: trunk/packages/babraham/fastqc/debian/control =================================================================== --- trunk/packages/babraham/fastqc/debian/control (rev 0) +++ trunk/packages/babraham/fastqc/debian/control 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,29 @@ +Source: fastqc +Section: science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0), libsam-java, default-jdk +Standards-Version: 3.9.3 +Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +Vcs-Svn: http://svn.debian.org/wsvn/debian-med/trunk/packages/babraham/fastqc/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/babraham/fastqc/ + +Package: fastqc +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, libsam-java, default-jre +Description: quality control for high throughput sequence data + FastQC aims to provide a simple way to do some quality control checks on + raw sequence data coming from high throughput sequencing pipelines. It + provides a modular set of analyses which you can use to give a quick + impression of whether your data has any problems of which you should + be aware before doing any further analysis. + . + The main functions of FastQC are + * Import of data from BAM, SAM or FastQ files (any variant) + * Providing a quick overview to tell you in which areas there may + be problems + * Summary graphs and tables to quickly assess your data + * Export of results to an HTML based permanent report + * Offline operation to allow automated generation of reports without + running the interactive application + Added: trunk/packages/babraham/fastqc/debian/copyright =================================================================== --- trunk/packages/babraham/fastqc/debian/copyright (rev 0) +++ trunk/packages/babraham/fastqc/debian/copyright 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,28 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: fastqc +Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + +Files: * +Copyright: Simon Adrews <[email protected]> +License: GPL-3.0+ + +Files: debian/* +Copyright: 2012 Steffen Moeller <[email protected]> +License: GPL-3.0+ + +License: GPL-3.0+ + 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 3 of the License, or + (at your option) any later version. + . + This package 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. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". Added: trunk/packages/babraham/fastqc/debian/docs =================================================================== --- trunk/packages/babraham/fastqc/debian/docs (rev 0) +++ trunk/packages/babraham/fastqc/debian/docs 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,5 @@ +INSTALL.txt +LICENSE.txt +README.txt +README.txt +RELEASE_NOTES.txt Added: trunk/packages/babraham/fastqc/debian/menu =================================================================== --- trunk/packages/babraham/fastqc/debian/menu (rev 0) +++ trunk/packages/babraham/fastqc/debian/menu 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,2 @@ +?package(fastqc):needs="X11" section="Applications/Bioinformatics"\ + title="fastqc" command="/usr/bin/fastqc" Added: trunk/packages/babraham/fastqc/debian/patches/Makefile.patch =================================================================== --- trunk/packages/babraham/fastqc/debian/patches/Makefile.patch (rev 0) +++ trunk/packages/babraham/fastqc/debian/patches/Makefile.patch 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,24 @@ +Index: fastqc-0.10.0/Makefile +=================================================================== +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ fastqc-0.10.0/Makefile 2012-04-25 00:53:51.965638178 +0200 +@@ -0,0 +1,19 @@ ++ ++all: fastqc.jar ++ ++fastqc.jar: ++ javac -cp /usr/share/java/sam.jar:/usr/share/java/jbzip2.jar `find uk -name "*.java"` ++ jar cf fastqc.jar `find uk -name "*.class" -o -name "*.png"` ++ ++DESTDIR= ++PREFIX=/usr ++install: fastqc.jar ++ mkdir -p $(DESTDIR)$(PREFIX)/share/fastqc/ ++ cp fastqc fastqc.jar $(DESTDIR)$(PREFIX)/share/fastqc/ ++ chmod +x $(DESTDIR)$(PREFIX)/share/fastqc/fastqc ++ cp -r Contaminants Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/ ++ ++clean: ++ find . -name "*.jar" -o -name "*.class" | xargs -r rm ++ ++.PHONY: all install Added: trunk/packages/babraham/fastqc/debian/patches/fastqc.patch =================================================================== --- trunk/packages/babraham/fastqc/debian/patches/fastqc.patch (rev 0) +++ trunk/packages/babraham/fastqc/debian/patches/fastqc.patch 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,39 @@ +Index: fastqc-0.10.0/fastqc +=================================================================== +--- fastqc-0.10.0.orig/fastqc 2011-09-08 17:26:38.000000000 +0200 ++++ fastqc-0.10.0/fastqc 2012-04-25 00:37:59.306680038 +0200 +@@ -7,6 +7,8 @@ + # Check to see if they've mistakenly downloaded the source distribution + # since several people have made this mistake + ++print STDERR "RealBin: $RealBin\n"; ++ + if (-e "$RealBin/uk/ac/bbsrc/babraham/FastQC/FastQCApplication.java") { + die "This is the source distribution of FastQC. You need to get the compiled version if you want to run the program\n"; + } +@@ -17,12 +19,12 @@ + $delimiter = ';'; + } + ++my $JavaClasspathExtraDir="/usr/share/java"; ++ + if ($ENV{CLASSPATH}) { +- $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar"; +-} +-else { +- $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar"; ++ $ENV{CLASSPATH} .= "$delimiter"; + } ++$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar"; + + my @java_args; + my @files; +@@ -230,5 +232,5 @@ + + Any bugs in fastqc should be reported either to [email protected] + or in www.bioinformatics.bbsrc.ac.uk/bugzilla/ +- +- +\ No newline at end of file ++ ++ Added: trunk/packages/babraham/fastqc/debian/patches/series =================================================================== --- trunk/packages/babraham/fastqc/debian/patches/series (rev 0) +++ trunk/packages/babraham/fastqc/debian/patches/series 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,2 @@ +Makefile.patch +fastqc.patch Added: trunk/packages/babraham/fastqc/debian/rules =================================================================== --- trunk/packages/babraham/fastqc/debian/rules (rev 0) +++ trunk/packages/babraham/fastqc/debian/rules 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,13 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ Property changes on: trunk/packages/babraham/fastqc/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/babraham/fastqc/debian/source/format =================================================================== --- trunk/packages/babraham/fastqc/debian/source/format (rev 0) +++ trunk/packages/babraham/fastqc/debian/source/format 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/babraham/fastqc/debian/watch.ex =================================================================== --- trunk/packages/babraham/fastqc/debian/watch.ex (rev 0) +++ trunk/packages/babraham/fastqc/debian/watch.ex 2012-04-24 23:04:16 UTC (rev 10572) @@ -0,0 +1,23 @@ +# Example watch control file for uscan +# Rename this file to "watch" and then you can run the "uscan" command +# to check for upstream updates and more. +# See uscan(1) for format + +# Compulsory line, this is a version 3 file +version=3 + +# Uncomment to examine a Webpage +# <Webpage URL> <string match> +#http://www.example.com/downloads.php fastqc-(.*)\.tar\.gz + +# Uncomment to examine a Webserver directory +#http://www.example.com/pub/fastqc-(.*)\.tar\.gz + +# Uncommment to examine a FTP server +#ftp://ftp.example.com/pub/fastqc-(.*)\.tar\.gz debian uupdate + +# Uncomment to find new files on sourceforge, for devscripts >= 2.9 +# http://sf.net/fastqc/fastqc-(.*)\.tar\.gz + +# Uncomment to find new files on GooglePages +# http://example.googlepages.com/foo.html fastqc-(.*)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
