[med-svn] [gasic] 02/03: Add patch to use mason from seqan-apps

[Andreas Tille]

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tille pushed a commit to branch master
in repository gasic.

commit a27f41ceea0ea24810c1cf3fdd4fd91558edd0db
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 3 15:12:48 2014 +0100

    Add patch to use mason from seqan-apps
---
 debian/changelog                             |  5 +----
 debian/patches/fix_example_indentation.patch | 15 +++++++++++++++
 debian/patches/series                        |  2 ++
 debian/patches/use_seqan_mason.patch         | 17 +++++++++++++++++
 4 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d3ebd14..b05b336 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,5 @@
 gasic (0.0.r18-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #<bug>)
-  TODO: since there is a name conflict with mason and the Debian package
-  mason is something else than the seqan tool, the code needs to be patched
-  to find /usr/lib/seqan/bin/mason
+  * Initial release (Closes: #739509)
 
  -- Andreas Tille <tille at debian.org>  Sat, 08 Feb 2014 08:47:28 +0100
diff --git a/debian/patches/fix_example_indentation.patch b/debian/patches/fix_example_indentation.patch
new file mode 100644
index 0000000..48295d5
--- /dev/null
+++ b/debian/patches/fix_example_indentation.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 08 Feb 2014 08:47:28 +0100
+Description: Example contains wring indentation
+
+--- a/doc/example_script.py
++++ b/doc/example_script.py
+@@ -157,7 +157,7 @@ for it in range(5):
+         tools.run_mapper['bowtie'](index_name, dataset, SAM_name)
+ 
+ 	# estimate the true abundances and count unique reads
+-    SAM_pattern = './SAM/rep{num}_%s.sam'.format(num=it)
++	SAM_pattern = './SAM/rep{num}_%s.sam'.format(num=it)
+ 	total[it],mapped[it,:],est[it,:],err[it,:],p[it,:] = correct_abundances.similarity_correction(names, sim_matrix, SAM_pattern, 100)
+ 	unique[it,:] = correct_abundances.unique(names, SAM_pattern)
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9c23266
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+use_seqan_mason.patch
+fix_example_indentation.patch
diff --git a/debian/patches/use_seqan_mason.patch b/debian/patches/use_seqan_mason.patch
new file mode 100644
index 0000000..babff7b
--- /dev/null
+++ b/debian/patches/use_seqan_mason.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 08 Feb 2014 08:47:28 +0100
+Description: since there is a name conflict with mason and the Debian package
+  mason is something else than the seqan tool, the code needs to be patched
+  to find /usr/lib/seqan/bin/mason
+
+--- gasic.orig/core/tools.py
++++ gasic/core/tools.py
+@@ -115,7 +115,7 @@
+ # to create a seperate caller function for every scenario.
+ 
+ def run_mason_illumina(ref, out):
+-    command = "mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s"%(out,ref)
++    command = "/usr/lib/seqan/bin/mason illumina -N 10000 -hi 0 -hs 0 -n 72  -sq -o %s %s"%(out,ref)
+     print "Executing:",command
+     os.system(command)
+     # remove the needless SAM file

-- 
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