01/01: gnu: metabat: Update to 0.32.4-1.cbdca756.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 2c3eb4b85be765dadcb19d65507063de4cc9dde7
Author: Ben Woodcroft <address@hidden>
Date:   Tue Oct 4 21:58:28 2016 +1000

    gnu: metabat: Update to 0.32.4-1.cbdca756.
    
    * gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
    * gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
    * gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                       |    1 +
 gnu/packages/bioinformatics.scm                    |   31 ++++++++++++--------
 .../patches/metabat-remove-compilation-date.patch  |   16 ++++++++++
 3 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 2637791..42b95a8 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -691,6 +691,7 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/mcrypt-CVE-2012-4409.patch                      \
   %D%/packages/patches/mcrypt-CVE-2012-4426.patch                      \
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch                      \
+  %D%/packages/patches/metabat-remove-compilation-date.patch   \
   %D%/packages/patches/mhash-keygen-test-segfault.patch                \
   %D%/packages/patches/mpc123-initialize-ao.patch              \
   %D%/packages/patches/mplayer2-theora-fix.patch               \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cf20057..ac46fe4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3221,18 +3221,23 @@ form of assemblies or reads.")
                    license:cpl1.0))))     ; Open Bloom Filter
 
 (define-public metabat
-  (package
-    (name "metabat")
-    (version "0.26.3")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://bitbucket.org/berkeleylab/metabat/get/";
-                    version ".tar.bz2"))
-              (file-name (string-append name "-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg"))))
+  ;; We package from a git commit because compilation of the released version
+  ;; fails.
+  (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
+    (package
+      (name "metabat")
+      (version (string-append "0.32.4-1." (string-take commit 8)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://bitbucket.org/berkeleylab/metabat.git";)
+               (commit commit)))
+         (file-name (string-append name "-" version))
+         (sha256
+          (base32
+           "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
+         (patches (search-patches "metabat-remove-compilation-date.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -3299,7 +3304,7 @@ enables the study of individual organisms and their 
interactions.  MetaBAT is
 an automated metagenome binning software, which integrates empirical
 probabilistic distances of genome abundance and tetranucleotide frequency.")
    (license (license:non-copyleft "file://license.txt"
-                                  "See license.txt in the distribution."))))
+                                  "See license.txt in the distribution.")))))
 
 (define-public minced
   (package
diff --git a/gnu/packages/patches/metabat-remove-compilation-date.patch 
b/gnu/packages/patches/metabat-remove-compilation-date.patch
new file mode 100644
index 0000000..7672205
--- /dev/null
+++ b/gnu/packages/patches/metabat-remove-compilation-date.patch
@@ -0,0 +1,16 @@
+Remove the reference to the compilation date so that the build is
+reproducible.
+
+diff --git a/src/metabat.cpp b/src/metabat.cpp
+index 88e06de..c95cb1a 100644
+--- a/src/metabat.cpp
++++ b/src/metabat.cpp
+@@ -49,7 +49,7 @@ int main(int ac, char* av[]) {
+       po::notify(vm);
+ 
+       if (vm.count("help") || inFile.length() == 0 || outFile.length() == 0) {
+-              cerr << "\nMetaBAT: Metagenome Binning based on Abundance and 
Tetranucleotide frequency (version " << version << "; " << __DATE__ << " " << 
__TIME__ << ")" << endl;
++              cerr << "\nMetaBAT: Metagenome Binning based on Abundance and 
Tetranucleotide frequency (version " << version << "; unknown compilation 
date)" << endl;
+               cerr << "by Don Kang (address@hidden), Jeff Froula, Rob Egan, 
and Zhong Wang (address@hidden) \n" << endl;
+               cerr << desc << endl << endl;
+