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.

diff --git a/gnu/local.mk b/gnu/local.mk
index 2e40026..8c683b8 100644 (file)
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -846,7 +846,6 @@ dist_patch_DATA =                                           \
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch                      \
   %D%/packages/patches/mesa-skip-disk-cache-test.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/mhash-keygen-test-segfault.patch                \
   %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch                \

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 70418cd..37980f3 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3475,19 +3475,17 @@ form of assemblies or reads.")
 (define-public metabat
   (package
     (name "metabat")
-    (version "2.11.3")
+    (version "2.12.1")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://bitbucket.org/berkeleylab/metabat.git")
-             (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
-       (file-name (string-append name "-" version "-checkout"))
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
-       (patches (search-patches "metabat-remove-compilation-date.patch"
-                                "metabat-fix-compilation.patch"))))
+         "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
+       (patches (search-patches "metabat-fix-compilation.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

diff --git a/gnu/packages/patches/metabat-remove-compilation-date.patch b/gnu/packages/patches/metabat-remove-compilation-date.patch
deleted file mode 100644 (file)
index 7672205..0000000
--- a/gnu/packages/patches/metabat-remove-compilation-date.patch
+++ /dev/null
@@ -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;
-