gnu: metabat: Update to 2.11.1.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu/local.mk

@@ -840,6 +840,7 @@ dist_patch_DATA =						\
   %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		\
   %D%/packages/patches/mpc123-initialize-ao.patch		\

gnu/packages/bioinformatics.scm

@@ -3467,23 +3467,20 @@ (define-public mash
                    license:cpl1.0))))     ; Open Bloom Filter
 
 (define-public metabat
-  ;; We package from a git commit because compilation of the released version
+  (package
-  ;; fails.
+    (name "metabat")
-  (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
+    (version "2.11.1")
-    (package
+    (source
-      (name "metabat")
+     (origin
-      (version (string-append "0.32.4-1." (string-take commit 8)))
+       (method url-fetch)
-      (source
+       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-       (origin
+                           version ".tar.gz"))
-         (method git-fetch)
+       (file-name (string-append name "-" version ".tar.gz"))
-         (uri (git-reference
+       (sha256
-               (url "https://bitbucket.org/berkeleylab/metabat.git")
+        (base32
-               (commit commit)))
+         "0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9"))
-         (file-name (string-append name "-" version))
+       (patches (search-patches "metabat-remove-compilation-date.patch"
-         (sha256
+                                "metabat-fix-compilation.patch"))))
-          (base32
-           "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
-         (patches (search-patches "metabat-remove-compilation-date.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -3500,35 +3497,35 @@ (define-public metabat
                 "#include \"htslib/kseq.h\""))
              #t))
          (add-after 'unpack 'fix-scons
-            (lambda* (#:key inputs #:allow-other-keys)
+           (lambda* (#:key inputs #:allow-other-keys)
-              (substitute* "SConstruct"
+             (substitute* "SConstruct"
-                (("^htslib_dir = 'samtools'")
+               (("^htslib_dir += 'samtools'")
-                 (string-append "hitslib_dir = '"
+                (string-append "htslib_dir = '"
-                                (assoc-ref inputs "htslib")
+                               (assoc-ref inputs "htslib")
-                                "'"))
+                               "'"))
-                (("^samtools_dir = 'samtools'")
+               (("^samtools_dir = 'samtools'")
-                 (string-append "samtools_dir = '"
+                (string-append "samtools_dir = '"
-                                (assoc-ref inputs "htslib")
+                               (assoc-ref inputs "samtools")
-                                "'"))
+                               "'"))
-                (("^findStaticOrShared\\('bam', hts_lib")
+               (("^findStaticOrShared\\('bam', hts_lib")
-                 (string-append "findStaticOrShared('bam', '"
+                (string-append "findStaticOrShared('bam', '"
-                                (assoc-ref inputs "samtools")
+                               (assoc-ref inputs "samtools")
-                                "/lib'"))
+                               "/lib'"))
-                ;; Do not distribute README.
+               ;; Do not distribute README.
-                (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
+               (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
-              #t))
+             #t))
          (delete 'configure)
          (replace 'build
-                  (lambda* (#:key inputs outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
-                    (mkdir (assoc-ref outputs "out"))
+             (mkdir (assoc-ref outputs "out"))
-                    (zero? (system* "scons"
+             (zero? (system* "scons"
-                                    (string-append
+                             (string-append
-                                     "PREFIX="
+                              "PREFIX="
-                                     (assoc-ref outputs "out"))
+                              (assoc-ref outputs "out"))
-                                    (string-append
+                             (string-append
-                                     "BOOST_ROOT="
+                              "BOOST_ROOT="
-                                     (assoc-ref inputs "boost"))
+                              (assoc-ref inputs "boost"))
-                                    "install"))))
+                             "install"))))
          ;; Check and install are carried out during build phase.
          (delete 'check)
          (delete 'install))))
@@ -3549,8 +3546,8 @@ (define-public metabat
 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"
+    (license (license:non-copyleft "file://license.txt"
-                                  "See license.txt in the distribution.")))))
+                                   "See license.txt in the distribution."))))
 
 (define-public minced
   (package

gnu/packages/patches/metabat-fix-compilation.patch

@@ -0,0 +1,39 @@
+This patch changes metabat so that (1) it is not build statically, (2) it uses
+shared libraries rather than static libraries where possible.
+
+diff --git a/SConstruct b/SConstruct
+index 69cdc0a..ac99bcb 100644
+--- a/SConstruct
++++ b/SConstruct
+@@ -26,8 +26,6 @@ debug = ARGUMENTS.get('DEBUG', None)
+ build_flags = ['-Wall', '-g', '-std=c++11', '-fopenmp']
+ link_flags = ['-lstdc++', '-lm', '-fopenmp']
+ 
+-if platform.platform(True, True).find('Darwin') == -1:
+-    link_flags.extend(['-static', '-static-libgcc', '-static-libstdc++'])
+ 
+ if debug is None:
+     build_flags.extend(['-O3', '-DNDEBUG', '-Wno-unknown-pragmas', '-Wno-deprecated-declarations', '-Wno-overflow', '-Wno-unused-variable'])
+@@ -110,17 +108,17 @@ def findStaticOrShared( lib, testPaths, static_source_list, link_flag_list, stat
+     for path in testPaths:
+         if not os.path.isdir(path):
+             continue
++        for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
++            if os.path.isfile(testfile):
++                print "Found shared library %s as %s" % (lib, testfile)
++                link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
++                return
+         for suffix in staticSuffixes:
+             testfile = '%s/lib%s%s' % (path, lib, suffix)
+             if os.path.isfile(testfile):
+                 static_source_list.append(testfile)
+                 print "Found static library %s as %s" % (lib, testfile)
+                 return
+-        for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
+-            if os.path.isfile(testfile):
+-                print "Found shared library %s as %s" % (lib, testfile)
+-                link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
+-                return
+     print "Could not find library for %s!!! Looked in %s" % (lib, testPaths)
+     return
+