[med-svn] r15589 - in trunk/packages: . readseq2 readseq2/trunk readseq2/trunk/debian readseq2/trunk/debian/source
Andreas Tille
tille at moszumanska.debian.org
Sat Dec 21 16:20:45 UTC 2013
Author: tille
Date: 2013-12-21 16:20:45 +0000 (Sat, 21 Dec 2013)
New Revision: 15589
Added:
trunk/packages/readseq2/
trunk/packages/readseq2/trunk/
trunk/packages/readseq2/trunk/debian/
trunk/packages/readseq2/trunk/debian/README.debian
trunk/packages/readseq2/trunk/debian/changelog
trunk/packages/readseq2/trunk/debian/compat
trunk/packages/readseq2/trunk/debian/control
trunk/packages/readseq2/trunk/debian/copyright
trunk/packages/readseq2/trunk/debian/rules
trunk/packages/readseq2/trunk/debian/source/
trunk/packages/readseq2/trunk/debian/source/format
trunk/packages/readseq2/trunk/debian/upstream
trunk/packages/readseq2/trunk/debian/watch
Log:
Inject Java version of readseq since it is needed by rdp-classifier which in turn should be recommended by Qiime
Added: trunk/packages/readseq2/trunk/debian/README.debian
===================================================================
--- trunk/packages/readseq2/trunk/debian/README.debian (rev 0)
+++ trunk/packages/readseq2/trunk/debian/README.debian 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,7 @@
+readseq2 for DEBIAN
+-------------------
+
+This is the version of readseq which was rewritten in Java. The
+older C version is available as Debian package readseq as well.
+
+ -- Andreas Tille <tille at debian.org> Sat, 21 Dec 2013 16:55:29 +0100
Added: trunk/packages/readseq2/trunk/debian/changelog
===================================================================
--- trunk/packages/readseq2/trunk/debian/changelog (rev 0)
+++ trunk/packages/readseq2/trunk/debian/changelog 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,6 @@
+readseq2 (2.1.30-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Sat, 21 Dec 2013 16:55:29 +0100
+
Added: trunk/packages/readseq2/trunk/debian/compat
===================================================================
--- trunk/packages/readseq2/trunk/debian/compat (rev 0)
+++ trunk/packages/readseq2/trunk/debian/compat 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1 @@
+9
Added: trunk/packages/readseq2/trunk/debian/control
===================================================================
--- trunk/packages/readseq2/trunk/debian/control (rev 0)
+++ trunk/packages/readseq2/trunk/debian/control 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,26 @@
+Source: readseq2
+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 (>=0.25),
+ default-jdk
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/readseq2/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/readseq2/trunk/
+Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
+
+Package: readseq2
+Architecture: all
+Depends: ${misc:Depends},
+ ${java:Depends}
+Description: Conversion between sequence formats (Java version)
+ Reads and writes nucleic/protein sequences in various
+ formats. Data files may have multiple sequences.
+ Readseq is particularly useful as it automatically detects many
+ sequence formats, and converts between them.
+ .
+ This is the rewrite of the original C version which is available
+ as well in package `readme`.
+
Added: trunk/packages/readseq2/trunk/debian/copyright
===================================================================
--- trunk/packages/readseq2/trunk/debian/copyright (rev 0)
+++ trunk/packages/readseq2/trunk/debian/copyright 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,18 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Readseq
+Source: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
+Files-Excluded: lib/orgxml.jar
+
+Files: *
+Copyright: 2000-2010 D. Gilbert <gilbertd at bio.indiana.edu>
+ biology dept., indiana university
+License: PD
+ Anyone can use Readseq. There are no copyright restrictions,
+ it is in the PUBLIC DOMAIN.
+
+Files: debian/*
+Copyright: © 2013 Andreas Tille <tille at debian.org>
+License: GPLv2+
+ The Debian packaging is licensed under the GPL which is available at
+ `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/readseq2/trunk/debian/rules
===================================================================
--- trunk/packages/readseq2/trunk/debian/rules (rev 0)
+++ trunk/packages/readseq2/trunk/debian/rules 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+get-orig-source:
+ uscan --verbose --force-download --repack --repack-compression xz
Property changes on: trunk/packages/readseq2/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/readseq2/trunk/debian/source/format
===================================================================
--- trunk/packages/readseq2/trunk/debian/source/format (rev 0)
+++ trunk/packages/readseq2/trunk/debian/source/format 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/readseq2/trunk/debian/upstream
===================================================================
--- trunk/packages/readseq2/trunk/debian/upstream (rev 0)
+++ trunk/packages/readseq2/trunk/debian/upstream 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,11 @@
+Reference:
+ Author: Don Gilbert
+ Title: Sequence file format conversion with command-line readseq
+ Journal: Current Protocols in Bioinformatics
+ Year: 2003
+ Volume: Appendix 1
+ Pages: E
+ DOI: 10.1002/0471250953.bia01es00
+ PMID: 18428689
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bia01es00/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bia01es00/pdf
Added: trunk/packages/readseq2/trunk/debian/watch
===================================================================
--- trunk/packages/readseq2/trunk/debian/watch (rev 0)
+++ trunk/packages/readseq2/trunk/debian/watch 2013-12-21 16:20:45 UTC (rev 15589)
@@ -0,0 +1,5 @@
+version=3
+http://iubio.bio.indiana.edu/soft/molbio/readseq/java/old/readseq-([.\d]+)-src.zip
+
+# sf.net is not updated any more
+# http://sf.net/readseq/readseq-([.\d]+)-src\.zip
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