@@ 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 \
@@ 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)
@@ 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
-