branch core-updates-frozen updated: gnu: metabat: Update to 2.15.

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     new 0bf3c9a  gnu: metabat: Update to 2.15.
0bf3c9a is described below

commit 0bf3c9abaa1d069421575b5af6a49dae950736bf
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Dec 9 11:48:15 2021 +0100

    gnu: metabat: Update to 2.15.
    
    * gnu/packages/bioinformatics.scm (metabat): Update to 2.15.
    [source]: Remove patch.
    [build-system]: Use cmake-build-system.
    [arguments]: Adjust to new build system.
    * gnu/packages/patches/metabat-fix-compilation.patch: Remove file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    | 61 +++++++++-------------
 gnu/packages/patches/metabat-fix-compilation.patch | 39 --------------
 3 files changed, 24 insertions(+), 77 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 621dace..c559667 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1457,7 +1457,6 @@ dist_patch_DATA =                                         
\
   %D%/packages/patches/mesa-skip-tests.patch                   \
   %D%/packages/patches/mescc-tools-boot.patch                  \
   %D%/packages/patches/meson-allow-dirs-outside-of-prefix.patch        \
-  %D%/packages/patches/metabat-fix-compilation.patch           \
   %D%/packages/patches/mhash-keygen-test-segfault.patch                \
   %D%/packages/patches/minetest-add-MINETEST_MOD_PATH.patch    \
   %D%/packages/patches/mingw-w64-6.0.0-gcc.patch               \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0030969..6d83a4a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -60,7 +60,6 @@
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system ruby)
-  #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
   #:use-module (guix deprecation)
   #:use-module (gnu packages)
@@ -5401,7 +5400,7 @@ form of assemblies or reads.")
 (define-public metabat
   (package
     (name "metabat")
-    (version "2.12.1")
+    (version "2.15")
     (source
      (origin
        (method git-fetch)
@@ -5411,44 +5410,32 @@ form of assemblies or reads.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
-       (patches (search-patches "metabat-fix-compilation.patch"))))
-    (build-system scons-build-system)
-    (arguments
-     `(#:scons ,scons-python2
-       #:scons-flags
-       (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
-             (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
-       #:tests? #f ;; Tests are run during the build phase.
+         "0v3gsps0ypani14102z2y1a2wignhpf7s1h45mxmj5f783rkhqd9"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       ,#~(list (string-append "-Dzlib_LIB=" #$(this-package-input "zlib")
+                               "/lib/libz.so")
+                (string-append "-Dhtslib_LIB=" #$(this-package-input "htslib")
+                               "/lib/libhts.so")
+                (string-append "-DBOOST_ROOT=" #$(this-package-input "boost")))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-includes
+         (add-after 'unpack 'configure-version-file
            (lambda _
-             (substitute* "src/BamUtils.h"
-               (("^#include \"bam/bam\\.h\"")
-                "#include \"samtools/bam.h\"")
-               (("^#include \"bam/sam\\.h\"")
-                "#include \"samtools/sam.h\""))
-             (substitute* "src/KseqReader.h"
-               (("^#include \"bam/kseq\\.h\"")
-                "#include \"htslib/kseq.h\""))))
-         (add-after 'unpack 'fix-scons
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "SConstruct"
-               (("^htslib_dir += 'samtools'")
-                (string-append "htslib_dir = '"
-                               (assoc-ref inputs "htslib")
-                               "'"))
-               (("^samtools_dir = 'samtools'")
-                (string-append "samtools_dir = '"
-                               (assoc-ref inputs "samtools")
-                               "'"))
-               (("^findStaticOrShared\\('bam', hts_lib")
-                (string-append "findStaticOrShared('bam', '"
-                               (assoc-ref inputs "samtools")
-                               "/lib'"))
-               ;; Do not distribute README.
-               (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")))))))
+             (copy-file "metabat_version.h.in" "metabat_version.h")
+             (substitute* "metabat_version.h"
+               (("@_time_stamp@") "19700101")
+               (("@GIT_IS_DIRTY@") "0")
+               (("@GIT_RETRIEVED_STATE@") "0")
+               (("@GIT_HEAD_SHA1@") (string-append "v" ,version)))))
+         (add-after 'unpack 'do-not-use-bundled-libraries
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("include\\(cmake.*") ""))
+             (substitute* "src/CMakeLists.txt"
+               (("set\\(Boost.*") "")
+               (("add_dependencies.*") "")))))))
     (inputs
      `(("zlib" ,zlib)
        ("perl" ,perl)
diff --git a/gnu/packages/patches/metabat-fix-compilation.patch 
b/gnu/packages/patches/metabat-fix-compilation.patch
deleted file mode 100644
index 7086a96..0000000
--- a/gnu/packages/patches/metabat-fix-compilation.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-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
-