[med-svn] [salmon] 01/01: make build reproducible

[Michael Crusoe]

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

commit 61c1ffe01bc2047bbc9f6b347dd2d1e527177ac3
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sun Feb 7 03:58:51 2016 -0800

    make build reproducible
---
 debian/changelog                  |  6 ++++++
 debian/control                    |  2 +-
 debian/patches/reproducible-build | 22 ++++++++++++++++++++++
 debian/patches/series             |  1 +
 4 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 0272869..5653e35 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+salmon (0.4.2+ds1-2) UNRELEASED; urgency=medium
+
+  * Make build reproducible. 
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sun, 07 Feb 2016 03:58:27 -0800
+
 salmon (0.4.2+ds1-1) unstable; urgency=low
 
   * Initial release (Closes: #800339)
diff --git a/debian/control b/debian/control
index a26eaba..64fa39e 100644
--- a/debian/control
+++ b/debian/control
@@ -26,7 +26,7 @@ Build-Depends: debhelper (>= 9),
                libeigen3-dev
 Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/salmon.git
-Vcs-Git: https://anonscm.debian.org/debian-med/salmon.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/salmon.git
 Homepage: https://github.com/COMBINE-lab/salmon
 
 Package: salmon
diff --git a/debian/patches/reproducible-build b/debian/patches/reproducible-build
new file mode 100644
index 0000000..265ccd6
--- /dev/null
+++ b/debian/patches/reproducible-build
@@ -0,0 +1,22 @@
+Author: Chris Lamb <lamby at debian.org>
+Description: makes the build reproducible
+Forwarded: https://github.com/COMBINE-lab/salmon/pull/40
+--- salmon-0.4.2+ds1.orig/src/BuildSalmonIndex.cpp
++++ salmon-0.4.2+ds1/src/BuildSalmonIndex.cpp
+@@ -151,7 +151,6 @@ int salmonIndex(int argc, char* argv[])
+     bool useStreamingParser = true;
+ 
+     uint32_t saSampInterval = 1;
+-    uint32_t maxThreads = std::thread::hardware_concurrency();
+     uint32_t numThreads;
+ 
+     po::options_description generic("Command Line Options");
+@@ -160,7 +159,7 @@ int salmonIndex(int argc, char* argv[])
+     ("help,h", "produce help message")
+     ("transcripts,t", po::value<string>()->required(), "Transcript fasta file.")
+     ("index,i", po::value<string>()->required(), "Salmon index.")
+-    ("threads,p", po::value<uint32_t>(&numThreads)->default_value(maxThreads)->required(),
++    ("threads,p", po::value<uint32_t>(&numThreads)->default_value(2)->required(),
+                             "Number of threads to use (only used for computing bias features)")
+     ("sasamp,s", po::value<uint32_t>(&saSampInterval)->default_value(1)->required(),
+                             "The interval at which the suffix array should be sampled. "
diff --git a/debian/patches/series b/debian/patches/series
index 22910fd..94988cd 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ use-system-pkg-config-tbb
 0007-Remove-unnecessarily-linked-libraries.patch
 0008-Remove-salmon_core-lib.patch
 0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
+reproducible-build

-- 
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