From 690a904ad766dfecf78749d121af528a7a49fa77 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 31 Aug 2017 09:31:54 +0800
Subject: gnu: metabat: Update to 2.11.3.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch.  Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    | 16 ++++++-------
 gnu/packages/patches/metabat-fix-boost-issue.patch | 27 ----------------------
 3 files changed, 8 insertions(+), 36 deletions(-)
 delete mode 100644 gnu/packages/patches/metabat-fix-boost-issue.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 708b50e8b6..1becca3d30 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -841,7 +841,6 @@ dist_patch_DATA =						\
   %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-boost-issue.patch		\
   %D%/packages/patches/mhash-keygen-test-segfault.patch		\
   %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch		\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0df0ee41a..e3729537bb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3475,19 +3475,19 @@ form of assemblies or reads.")
 (define-public metabat
   (package
     (name "metabat")
-    (version "2.11.2")
+    (version "2.11.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/berkeleylab/metabat.git")
+             (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
+         "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
        (patches (search-patches "metabat-remove-compilation-date.patch"
-                                "metabat-fix-compilation.patch"
-                                "metabat-fix-boost-issue.patch"))))
+                                "metabat-fix-compilation.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/patches/metabat-fix-boost-issue.patch b/gnu/packages/patches/metabat-fix-boost-issue.patch
deleted file mode 100644
index 3382d84d66..0000000000
--- a/gnu/packages/patches/metabat-fix-boost-issue.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-This patch fixes the issue described at
-https://bitbucket.org/berkeleylab/metabat/issues/28/compilation-fail-with-boost-164
-
-diff --git a/src/metabat.h b/src/metabat.h
-index 32ae94c..2292c04 100644
---- a/src/metabat.h
-+++ b/src/metabat.h
-@@ -35,6 +35,7 @@ KSEQ_INIT(gzFile, gzread)
- 
- #include <boost/program_options.hpp>
- #include <boost/algorithm/string.hpp>
-+#include <boost/serialization/array_wrapper.hpp>
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/math/distributions.hpp>
- #include <boost/serialization/serialization.hpp>
-diff --git a/src/metabat2.h b/src/metabat2.h
-index 60a9998..19fa815 100644
---- a/src/metabat2.h
-+++ b/src/metabat2.h
-@@ -41,6 +41,7 @@ KSEQ_INIT(gzFile, gzread)
- 
- #include <boost/program_options.hpp>
- #include <boost/algorithm/string.hpp>
-+#include <boost/serialization/array_wrapper.hpp>
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/numeric/ublas/matrix_sparse.hpp>
- #include <boost/numeric/ublas/matrix_proxy.hpp>
-- 
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