From 2c3eb4b85be765dadcb19d65507063de4cc9dde7 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Tue, 4 Oct 2016 21:58:28 +1000
Subject: 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(-)
 create mode 100644 gnu/packages/patches/metabat-remove-compilation-date.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 2637791b81..42b95a881e 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 cf20057bcd..ac46fe4bcc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3221,18 +3221,23 @@ (define-public mash
                    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 @@ (define-public metabat
 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 0000000000..7672205b22
--- /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 (ddkang@lbl.gov), Jeff Froula, Rob Egan, and Zhong Wang (zhongwang@lbl.gov) \n" << endl;
+ 		cerr << desc << endl << endl;
+ 
-- 
cgit v1.2.3