[med-svn] [trinityrnaseq] 08/09: switch to bowtie2; disable version check

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 41489bc5a66af085d22aa1a19c466ed06de4408e
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 05:53:43 2016 -0800

    switch to bowtie2; disable version check
---
 debian/control                       |  2 +-
 debian/copyright                     |  1 +
 debian/patches/disable-version-check | 13 +++++++++++++
 debian/patches/series                |  1 +
 4 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index d47d008..d0043db 100644
--- a/debian/control
+++ b/debian/control
@@ -27,7 +27,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${perl:Depends},
          ${java:Depends},
-         bowtie,
+         bowtie2,
          python,
          libwww-perl,
          default-jre-headless,
diff --git a/debian/copyright b/debian/copyright
index ca490ce..3dd4c62 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -15,6 +15,7 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  trinity-plugins/htslib*tar*
  trinity-plugins/samtools*
  trinity-plugins/slclust/Makefile.bak
+ galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc
diff --git a/debian/patches/disable-version-check b/debian/patches/disable-version-check
new file mode 100644
index 0000000..a3b388a
--- /dev/null
+++ b/debian/patches/disable-version-check
@@ -0,0 +1,13 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: Disable the version "phone home" for privacy
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -552,7 +552,7 @@
+ 
+ my $ANANAS_DIR = "";
+ 
+-my $NO_VERSION_CHECK = 0;
++my $NO_VERSION_CHECK = 1;
+ 
+ 
+ &GetOptions( 
diff --git a/debian/patches/series b/debian/patches/series
index 68d9373..ab49bc3 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -11,3 +11,4 @@ fix_system_paths
 hardening
 reproducible-build
 scaffold_iworm_contigs-Makefile-fix-clean
+disable-version-check

-- 
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