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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.
wip-deploy
Ben Woodcroft 5 years ago
parent
commit
2c3eb4b85b
No known key found for this signature in database GPG Key ID: E44DCCD146E0CCF4
  1. 1
      gnu/local.mk
  2. 31
      gnu/packages/bioinformatics.scm
  3. 16
      gnu/packages/patches/metabat-remove-compilation-date.patch

1
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 \

31
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

16
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;
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