[med-svn] r10931 - in trunk/packages/qiime/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Mon May 21 21:22:05 UTC 2012 

Author: tille
Date: 2012-05-21 21:22:05 +0000 (Mon, 21 May 2012)
New Revision: 10931

Removed:
   trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch
Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/control
   trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
   trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
   trunk/packages/qiime/trunk/debian/patches/series
   trunk/packages/qiime/trunk/debian/qiime.links
Log:
Adapted patches to new upstream version; link king.jar


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/changelog	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1,11 +1,14 @@
 qiime (1.5.0-1) UNRELEASED; urgency=low
 
-  * New upstream version
+  * New upstream version (adapted patches + remove patch that was applied
+    upstream)
   * debian/get-orig-source: Strip *.jar file from upstream source which
     should never have been there
   * debian/upstream:
      - more complete authors information in BibTeX conform format
      - Moved DOI+PMID to References
+  * debian/qiime.links: Link to king.jar
+  * debian/control: Depends: king
 
  -- Andreas Tille <tille at debian.org>  Tue, 08 May 2012 18:07:56 +0200
 

Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/control	2012-05-21 21:22:05 UTC (rev 10931)
@@ -16,7 +16,8 @@
 Package: qiime
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
- python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 )
+ python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 ),
+ king
 Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal,
  fasttree, ampliconnoise, python-matplotlib, python-numpy
 Suggests: t-coffee, cytoscape

Modified: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1,5 +1,5 @@
---- Qiime-1.4.0.orig/qiime/denoiser/utils.py
-+++ Qiime-1.4.0/qiime/denoiser/utils.py
+--- Qiime-1.5.0.orig/qiime/denoiser/utils.py
++++ Qiime-1.5.0/qiime/denoiser/utils.py
 @@ -41,9 +41,12 @@
  def get_flowgram_ali_exe():
      """Return the path to the flowgram alignment prog

Deleted: trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1,49 +0,0 @@
-Description: GHC 7.4.2 compatibility
- This patch changes the module imports so that it works without the haskell2012
- library, which is hidden with GHC 7.4.1 by default.
-Author: Joachim Breitner <nomeata at debian.org>
-Date: Mon, 19 Mar 2012 15:26:02 +0100
-Bug-Debian: http://bugs.debian.org/663889
-Forewarded: Jens Reeder <jens.reeder at gmail.com>
-
---- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
-+++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
-@@ -1,6 +1,6 @@
- > module FlowgramUtils where
- 
--> import Array
-+> import Data.Array
- > import System.IO.Unsafe (unsafePerformIO)
- 
- > type FlowSignalDistrib = Array (Int,Int) Float
---- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
-+++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
-@@ -1,13 +1,12 @@
- > module Main where
- 
--> import Array
--> import List
-+> import Data.Array
-+> import Data.List
- > import FlowgramUtils
- > import ADPCombinators
--> import System(getArgs)
-+> import System.Environment(getArgs)
- > import System.IO
--> import System.Exit(exitWith)
--> import System
-+> import System.Exit(exitWith, ExitCode(..))
- > import Text.Printf(printf)
- 
- The signature:
---- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
-+++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
-@@ -7,7 +7,7 @@
- ----------------------------------------------------------------------
- 
- > module ADPCombinators where
--> import Array
-+> import Data.Array
- 
- Lexical parsers
- ----------------

Modified: trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1,5 +1,5 @@
---- Qiime-1.4.0.orig/qiime/trim_sff_primers.py
-+++ Qiime-1.4.0/qiime/trim_sff_primers.py
+--- Qiime-1.5.0.orig/qiime/trim_sff_primers.py
++++ Qiime-1.5.0/qiime/trim_sff_primers.py
 @@ -101,8 +101,8 @@
          clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
          

Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/patches/series	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1,3 +1,2 @@
 python26_trim_sff_primers.patch
 fix_binary_helper_location.patch
-ghc_7.4.2_compatibility.patch

Modified: trunk/packages/qiime/trunk/debian/qiime.links
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.links	2012-05-21 20:42:58 UTC (rev 10930)
+++ trunk/packages/qiime/trunk/debian/qiime.links	2012-05-21 21:22:05 UTC (rev 10931)
@@ -1 +1,2 @@
-usr/bin/qiime	usr/bin/denoiser
+usr/bin/qiime		usr/bin/denoiser
+usr/share/java/king.jar	usr/lib/qiime/support_files/jar/king.jar

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