[med-svn] r10572 - in trunk/packages: . babraham babraham/fastqc babraham/fastqc/debian babraham/fastqc/debian/patches babraham/fastqc/debian/source
Steffen Möller
moeller at alioth.debian.org
Tue Apr 24 23:04:16 UTC 2012
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <simon.andrews at bbsrc.ac.uk>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+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 simon.andrews at babraham.ac.uk
+ 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
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