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

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* 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.
This commit is contained in:
Ben Woodcroft 2016-10-04 21:58:28 +10:00
parent 47c14714a4
commit 2c3eb4b85b
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GPG key ID: E44DCCD146E0CCF4
3 changed files with 35 additions and 13 deletions
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1
gnu/local.mk
View file

@ -691,6 +691,7 @@ dist_patch_DATA = \
%D%/packages/patches/mcrypt-CVE-2012-4409.patch \ %D%/packages/patches/mcrypt-CVE-2012-4409.patch \
%D%/packages/patches/mcrypt-CVE-2012-4426.patch \ %D%/packages/patches/mcrypt-CVE-2012-4426.patch \
%D%/packages/patches/mcrypt-CVE-2012-4527.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/mhash-keygen-test-segfault.patch \
%D%/packages/patches/mpc123-initialize-ao.patch \ %D%/packages/patches/mpc123-initialize-ao.patch \
%D%/packages/patches/mplayer2-theora-fix.patch \ %D%/packages/patches/mplayer2-theora-fix.patch \

31
gnu/packages/bioinformatics.scm
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@ -3221,18 +3221,23 @@ (define-public mash
license:cpl1.0)))) ; Open Bloom Filter license:cpl1.0)))) ; Open Bloom Filter
(define-public metabat (define-public metabat
(package ;; We package from a git commit because compilation of the released version
(name "metabat") ;; fails.
(version "0.26.3") (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
(source (origin (package
(method url-fetch) (name "metabat")
(uri (string-append (version (string-append "0.32.4-1." (string-take commit 8)))
"https://bitbucket.org/berkeleylab/metabat/get/" (source
version ".tar.bz2")) (origin
(file-name (string-append name "-" version ".tar.bz2")) (method git-fetch)
(sha256 (uri (git-reference
(base32 (url "https://bitbucket.org/berkeleylab/metabat.git")
"1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg")))) (commit commit)))
(file-name (string-append name "-" version))
(sha256
(base32
"0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
(patches (search-patches "metabat-remove-compilation-date.patch"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:phases `(#:phases
@ -3299,7 +3304,7 @@ (define-public metabat
an automated metagenome binning software, which integrates empirical an automated metagenome binning software, which integrates empirical
probabilistic distances of genome abundance and tetranucleotide frequency.") probabilistic distances of genome abundance and tetranucleotide frequency.")
(license (license:non-copyleft "file://license.txt" (license (license:non-copyleft "file://license.txt"
"See license.txt in the distribution.")))) "See license.txt in the distribution.")))))
(define-public minced (define-public minced
(package (package

16
gnu/packages/patches/metabat-remove-compilation-date.patch Normal file
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@ -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;