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gnu: metabat: Update to 2.12.1. 

* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it.  Use url-fetch.
This commit is contained in:
Ben Woodcroft 2017-09-01 13:59:28 +08:00
parent 43d01672a1
commit 25bd1fc1c1
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GPG Key ID: 2A6AD9F4AAC20DF6
3 changed files with 7 additions and 26 deletions
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1
gnu/local.mk
View File

@ -846,7 +846,6 @@ dist_patch_DATA = \
%D%/packages/patches/mcrypt-CVE-2012-4527.patch \ %D%/packages/patches/mcrypt-CVE-2012-4527.patch \
%D%/packages/patches/mesa-skip-disk-cache-test.patch \ %D%/packages/patches/mesa-skip-disk-cache-test.patch \
%D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch \ %D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch \
%D%/packages/patches/metabat-remove-compilation-date.patch \
%D%/packages/patches/metabat-fix-compilation.patch \ %D%/packages/patches/metabat-fix-compilation.patch \
%D%/packages/patches/mhash-keygen-test-segfault.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \
%D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch \ %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch \

16
gnu/packages/bioinformatics.scm
View File

@ -3475,19 +3475,17 @@ form of assemblies or reads.")
(define-public metabat (define-public metabat
(package (package
(name "metabat") (name "metabat")
(version "2.11.3") (version "2.12.1")
(source (source
(origin (origin
(method git-fetch) (method url-fetch)
(uri (git-reference (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
(url "https://bitbucket.org/berkeleylab/metabat.git") version ".tar.gz"))
(commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c"))) (file-name (string-append name "-" version ".tar.gz"))
(file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww")) "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
(patches (search-patches "metabat-remove-compilation-date.patch" (patches (search-patches "metabat-fix-compilation.patch"))))
"metabat-fix-compilation.patch"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:phases `(#:phases

16
gnu/packages/patches/metabat-remove-compilation-date.patch
View File

@ -1,16 +0,0 @@
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;