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| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-10-04 21:58:28 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-10-04 22:02:52 +1000 |
| commit | 2c3eb4b85be765dadcb19d65507063de4cc9dde7 (patch) | |
| tree | 56e9b17b6554b235ab7d0478879398df422cbd00 /gnu | |
| parent | 47c14714a400c912243a79c421e0f0cfd4a0d55d (diff) | |
| download | patches-2c3eb4b85be765dadcb19d65507063de4cc9dde7.tar patches-2c3eb4b85be765dadcb19d65507063de4cc9dde7.tar.gz | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 | ||||
| -rw-r--r-- | gnu/packages/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 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 @@ 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 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; + |