[med-svn] [bbmap] 02/02: Initial packaging

[Andreas Tille]

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tille pushed a commit to branch master
in repository bbmap.

commit 39014a2a9d5055bb490c178dea63ebd034736be7
Author: Andreas Tille <tille at debian.org>
Date:   Sat Mar 19 09:12:24 2016 +0100

    Initial packaging
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 36 ++++++++++++++++++++++++++++++++++++
 debian/copyright     | 12 ++++++++++++
 debian/install       |  1 +
 debian/manifest      |  6 ++++++
 debian/rules         | 24 ++++++++++++++++++++++++
 debian/source/format |  1 +
 debian/watch         |  5 +++++
 9 files changed, 91 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..3925ef1
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bbmap (35.85+dfsg-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 18 Mar 2016 13:50:56 +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..5d50ac9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,36 @@
+Source: bbmap
+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),
+               javahelper,
+               default-jdk
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bbmap.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/bbmap.git
+Homepage: https://sourceforge.net/projects/bbmap/
+
+Package: bbmap
+Architecture: all
+Depends: ${java:Depends},
+         ${misc:Depends}
+Description: short read aligner, and other bioinformatic tools.
+ BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
+ arbitrarily large genomes with millions of scaffolds. Handles Illumina,
+ PacBio, 454, and other reads; very high sensitivity and tolerant of
+ errors and numerous large indels.
+ .
+ BBMap is multithreaded as well as the other tools bundled into this
+ package for instance:
+ .
+ BBNorm: Kmer-based error-correction and normalization tool.
+ .
+ Dedupe: Simplifies assemblies by removing duplicate or contained
+ subsequences that share a target percent identity.
+ .
+ Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam,
+ interleaved/paired, and ASCII-33/64, at over 500 MB/s.
+ .
+ BBDuk: Filters, trims, or masks reads with kmer matches to an
+ artifact/contaminant file.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fc23ab2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,12 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BBmap
+Source: https://sourceforge.net/projects/bbmap/
+Files-Excluded: *.class
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..d4f14ab
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+*.jar	usr/share/java
diff --git a/debian/manifest b/debian/manifest
new file mode 100644
index 0000000..1d311b2
--- /dev/null
+++ b/debian/manifest
@@ -0,0 +1,6 @@
+/usr/share/java/bbmap.jar:
+ Main-Class: current/align2/BBMap
+ Class-Path: /usr/share/java/mpj.jar
+
+
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..440e01b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+JAVA_HOME  := /usr/lib/jvm/default-java
+DEBJAR    := /usr/share/java
+CLASS_PATH := $(DEBJAR)/mpj.jar
+
+%:
+	dh $@ --with javahelper
+
+override_dh_auto_clean:
+	# do nothing
+
+override_dh_clean:
+	dh_clean
+	find . -name "*.class" -delete
+
+override_dh_auto_build:
+	echo "Manual build"
+	javac -classpath $(CLASS_PATH) `find current -name "*.java"` && \
+	jar -cmf debian/manifest $(DEBPKGNAME).jar `find current -name "*.class"`
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/watch b/debian/watch
new file mode 100644
index 0000000..b616ee2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  http://sf.net/bbmap/BBMap_(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+

-- 
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