[med-svn] [qualimap] 02/02: Add initial Debian packaging
Andreas Tille
tille at debian.org
Tue Nov 17 13:54:03 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository qualimap.
commit 5e0672783f62e73f608a5dafddccc75c057e46fc
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 17 14:49:25 2015 +0100
Add initial Debian packaging
---
debian/changelog | 6 ++++++
debian/compat | 1 +
debian/control | 46 +++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 27 +++++++++++++++++++++++++
debian/maven.cleanIgnoreRules | 1 +
debian/maven.ignoreRules | 5 +++++
debian/maven.publishedRules | 3 +++
debian/maven.rules | 5 +++++
debian/qualimap.poms | 28 ++++++++++++++++++++++++++
debian/rules | 22 +++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++++
debian/watch | 4 ++++
13 files changed, 161 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..3f577f0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+qualimap (2.1.3+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+ TODO: git://anonscm.debian.org/pkg-java/libejml-java.git
+
+ -- Andreas Tille <tille at debian.org> Tue, 17 Nov 2015 14:47:59 +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..522e56b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,46 @@
+Source: qualimap
+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 (>= 9),
+ picard-tools,
+ libsam-java
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/qualimap.git
+Vcs-Git: git://anonscm.debian.org/debian-med/qualimap.git
+Homepage: http://qualimap.bioinfo.cipf.es/
+
+Package: qualimap
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: evaluating next generation sequencing alignment data
+ Qualimap 2 provides both a Graphical User Inteface (GUI) and a command-
+ line interface to facilitate the quality control of alignment sequencing
+ data and its derivatives like feature counts.
+ .
+ Supported types of experiments include:
+ * Whole-genome sequencing
+ * Whole-exome sequencing
+ * RNA-seq (speical mode available)
+ * ChIP-seq
+ .
+ Qualimap examines sequencing alignment data in SAM/BAM files according
+ to the features of the mapped reads and provides an overall view of the
+ data that helps to the detect biases in the sequencing and/or mapping of
+ the data and eases decision-making for further analysis.
+ .
+ Qualimap provides multi-sample comparison of alignment and counts data.
+ * Fast analysis accross the reference of genome coverage and nucleotide
+ distribution;
+ * Easy to interpret summary of the main properties of the
+ alignment data;
+ * Analysis of the reads mapped inside/outside of the regions provided
+ in GFF format;
+ * Computation and analysis of read counts obtained from intersectition
+ of read alignments with genomic features;
+ * Analysis of the adequasy of the sequencing depth in RNA-seq
+ experiments;
+ * Multi-sample comparison of alignment and counts data;
+ * Clustering of epigenomic profiles.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7696834
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: QualiMap
+Upstream-Contact: https://groups.google.com/forum/#!forum/qualimap
+Source: http://qualimap.bioinfo.cipf.es/
+Files-Excluded: *.jar
+
+Files: *
+Copyright: 2008-2015 Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2015 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 the full text of the GNU General Public
+ License version 2 or later at /usr/share/common-licenses/GPL-2.
diff --git a/debian/maven.cleanIgnoreRules b/debian/maven.cleanIgnoreRules
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/debian/maven.cleanIgnoreRules
@@ -0,0 +1 @@
+
diff --git a/debian/maven.ignoreRules b/debian/maven.ignoreRules
new file mode 100644
index 0000000..38b09b3
--- /dev/null
+++ b/debian/maven.ignoreRules
@@ -0,0 +1,5 @@
+
+com.mycila.maven-license-plugin maven-license-plugin * * * *
+com.oracle javafx * * * *
+org.bioinfo bioinfo-formats * * * *
+org.biojava nbio * * * *
diff --git a/debian/maven.publishedRules b/debian/maven.publishedRules
new file mode 100644
index 0000000..1d5fa89
--- /dev/null
+++ b/debian/maven.publishedRules
@@ -0,0 +1,3 @@
+
+org.bioinfo.ngs qualimap jar * * *
+org.bioinfo.ngs qualimap jar s/.*/debian/ * *
diff --git a/debian/maven.rules b/debian/maven.rules
new file mode 100644
index 0000000..710352e
--- /dev/null
+++ b/debian/maven.rules
@@ -0,0 +1,5 @@
+
+junit junit jar s/4\..*/4.x/ * *
+org.bioinfo.ngs qualimap jar * * *
+org.bioinfo.ngs qualimap jar s/.*/debian/ * *
+s/org.bioinfo/org.biojava/ s/bioinfo-ngs/nbio/ * s/.*/debian/ * *
diff --git a/debian/qualimap.poms b/debian/qualimap.poms
new file mode 100644
index 0000000..4c16dce
--- /dev/null
+++ b/debian/qualimap.poms
@@ -0,0 +1,28 @@
+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]*
+# where option can be:
+# --ignore: ignore this POM and its artifact if any
+# --ignore-pom: don't install the POM. To use on POM files that are created
+# temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
+# --no-parent: remove the <parent> tag from the POM
+# --package=<package>: an alternative package to use when installing this POM
+# and its artifact
+# --has-package-version: to indicate that the original version of the POM is the same as the upstream part
+# of the version for the package.
+# --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
+# during a clean operation with mh_cleanpom or mh_installpom
+# --artifact=<path>: path to the build artifact associated with this POM,
+# it will be installed when using the command mh_install. [mh_install]
+# --java-lib: install the jar into /usr/share/java to comply with Debian
+# packaging guidelines
+# --usj-name=<name>: name to use when installing the library in /usr/share/java
+# --usj-version=<version>: version to use when installing the library in /usr/share/java
+# --no-usj-versionless: don't install the versionless link in /usr/share/java
+# --dest-jar=<path>: the destination for the real jar.
+# It will be installed with mh_install. [mh_install]
+# --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
+# --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
+# Empty by default. [mh_install]
+#
+pom.xml
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..20b26a5
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/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))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compress xz
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..9d3cdab
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Fernando García-Alcalde and Konstantin Okonechnikov and José Carbonell and Luis M. Cruz and Stefan Götz and Sonia Tarazona and Joaquín Dopazo and Thomas F. Meyer and Ana Conesa
+ Title: "Qualimap: evaluating next-generation sequencing alignment data"
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 20
+ Pages: 2678-2679
+ DOI: 10.1093/bioinformatics/bts503
+ PMID: 22914218
+ URL: http://bioinformatics.oxfordjournals.org/content/28/20/2678
+ eprint: http://bioinformatics.oxfordjournals.org/content/28/20/2678.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e8cbf3e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://bitbucket.org/kokonech/qualimap/downloads .*/qualimap_v(\d\S*)_src\.zip
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qualimap.git
More information about the debian-med-commit
mailing list