[med-svn] [transdecoder] 01/01: Make the sample data reproducible

[Michael Crusoe]

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

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

commit b2d2b5c57de30934cc09cc4180cec7f1f810a8dc
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Apr 23 11:01:40 2016 -0700

    Make the sample data reproducible
---
 debian/changelog                              | 12 ++++++++++++
 debian/control                                |  6 +++---
 debian/patches/reproducible-sample_data.patch | 16 ++++++++++++++++
 debian/patches/series                         |  1 +
 4 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 6cea07a..61f9a4a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+transdecoder (2.0.1+dfsg-3) unstable; urgency=medium
+
+  [ Eduard Sanou ]
+  * Set a hash seed for Perl before generating sample_data/transcripts.fasta
+    to get a reproducible output. Closes: #822268
+
+  [ Michael R. Crusoe ]
+  * Updated VCS URLs, bumped standards version, forwarded Eduard's patch
+    upstream.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sun, 24 Apr 2016 11:53:12 -0700
+
 transdecoder (2.0.1+dfsg-2) unstable; urgency=medium
 
   [ Andreas Tille ]
diff --git a/debian/control b/debian/control
index 538244d..6cc14fa 100644
--- a/debian/control
+++ b/debian/control
@@ -1,15 +1,15 @@
 Source: transdecoder
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>,
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                cd-hit,
                liburi-perl
-Standards-Version: 3.9.6
+Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git
-Vcs-Git: git://anonscm.debian.org/debian-med/transdecoder.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/transdecoder.git
 Homepage: https://transdecoder.github.io/
 
 Package: transdecoder
diff --git a/debian/patches/reproducible-sample_data.patch b/debian/patches/reproducible-sample_data.patch
new file mode 100644
index 0000000..773faec
--- /dev/null
+++ b/debian/patches/reproducible-sample_data.patch
@@ -0,0 +1,16 @@
+Description: Make the sample data reproducible
+ Set a fixed hash seed for Perl before generating sample_data/transcripts.fasta
+ to get reproducible results
+Author: Eduard Sanou <dhole at openmailbox.org>
+Forwarded: https://github.com/TransDecoder/TransDecoder/pull/20
+--- transdecoder-2.0.1+dfsg.orig/sample_data/runMe.sh
++++ transdecoder-2.0.1+dfsg/sample_data/runMe.sh
+@@ -26,7 +26,7 @@ fi
+ ../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3
+ 
+ ## generate transcripts fasta file
+-../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta 
++PERL_HASH_SEED=0 ../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta 
+ 
+ ## Extract the long ORFs
+ ../TransDecoder.LongOrfs -t transcripts.fasta
diff --git a/debian/patches/series b/debian/patches/series
index 07cfd4f..8488ccc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 cd-hit-est-rename
 fix-whatis
 reproducible-build
+reproducible-sample_data.patch

-- 
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