[med-svn] r22141 - trunk/packages/snpeff/trunk/debian

[Andreas Tille]

Author: tille
Date: 2016-06-20 19:48:09 +0000 (Mon, 20 Jun 2016)
New Revision: 22141

Modified:
   trunk/packages/snpeff/trunk/debian/changelog
   trunk/packages/snpeff/trunk/debian/control
   trunk/packages/snpeff/trunk/debian/copyright
   trunk/packages/snpeff/trunk/debian/watch
Log:
Source is actually at Github, we need to strip several files (probably more); Vcs will be moved to Git


Modified: trunk/packages/snpeff/trunk/debian/changelog
===================================================================
--- trunk/packages/snpeff/trunk/debian/changelog	2016-06-20 15:01:19 UTC (rev 22140)
+++ trunk/packages/snpeff/trunk/debian/changelog	2016-06-20 19:48:09 UTC (rev 22141)
@@ -1,4 +1,4 @@
-snpeff (4.3-1) UNRELEASED; urgency=low
+snpeff (4.2+dfsg-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #<bug>)
 

Modified: trunk/packages/snpeff/trunk/debian/control
===================================================================
--- trunk/packages/snpeff/trunk/debian/control	2016-06-20 15:01:19 UTC (rev 22140)
+++ trunk/packages/snpeff/trunk/debian/control	2016-06-20 19:48:09 UTC (rev 22141)
@@ -1,18 +1,19 @@
 Source: snpeff
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.4
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snpeff.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/snpeff.git
 Homepage: http://snpeff.sourceforge.net/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/snpeff/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/snpeff/trunk/
 
 Package: snpeff
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: annotation and effect prediction tool for genome sequences
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: genetic variant annotation and effect prediction toolbox
  SnpEff is a variant annotation and effect prediction tool. It annotates
  and predicts the effects of variants on genes (such as amino acid
  changes). 

Modified: trunk/packages/snpeff/trunk/debian/copyright
===================================================================
--- trunk/packages/snpeff/trunk/debian/copyright	2016-06-20 15:01:19 UTC (rev 22140)
+++ trunk/packages/snpeff/trunk/debian/copyright	2016-06-20 19:48:09 UTC (rev 22141)
@@ -1,10 +1,16 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: snpEff
 Upstream-Contact: Pablo Cingolani <pcingola at users.sourceforge.net>
-Source: https://snpeff.svn.sourceforge.net/svnroot/snpeff/SnpEffect/trunk/
+Source: https://github.com/pcingola/SnpEff/releases
+Files-Excluded: */config/OLD
+                */doc/*.pdf
+                */doc/hgvs
+                *.jar
+                */papers/*.pdf
+                */scripts_build/OLD
 
 Files: *
-Copyright: © 2008-2012, Pablo Cingolani <pcingola at users.sourceforge.net>
+Copyright: © 2008-2016, Pablo Cingolani <pcingola at users.sourceforge.net>
 License: LGPLv3
 
 Files: debian/*

Modified: trunk/packages/snpeff/trunk/debian/watch
===================================================================
--- trunk/packages/snpeff/trunk/debian/watch	2016-06-20 15:01:19 UTC (rev 22140)
+++ trunk/packages/snpeff/trunk/debian/watch	2016-06-20 19:48:09 UTC (rev 22141)
@@ -1,4 +1,8 @@
 version=3
 
-opts="uversionmangle=s/_/./g" \
-  http://sf.net/snpeff/snpEff_v(\d[\d_.]+)_core\.(?:tgz|tbz|txz|zip|(?:tar\.(?:gz|bz2|xz)))
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+   https://github.com/pcingola/SnpEff/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+# That's the binary jar download
+#opts="uversionmangle=s/_/./g" \
+#  http://sf.net/snpeff/snpEff_v(\d[\d_.]+)_core\.(?:tgz|tbz|txz|zip|(?:tar\.(?:gz|bz2|xz)))