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.
This commit is contained in:
Ben Woodcroft 2017-07-15 16:31:40 +10:00
parent 897ab082b2
commit f3f68a442c
No known key found for this signature in database
GPG key ID: 2A6AD9F4AAC20DF6
3 changed files with 83 additions and 46 deletions

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@ -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 \

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@ -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
;; fails.
(let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
(package
(name "metabat")
(version (string-append "0.32.4-1." (string-take commit 8)))
(version "2.11.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://bitbucket.org/berkeleylab/metabat.git")
(commit commit)))
(file-name (string-append name "-" version))
(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
"0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
(patches (search-patches "metabat-remove-compilation-date.patch"))))
"0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9"))
(patches (search-patches "metabat-remove-compilation-date.patch"
"metabat-fix-compilation.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -3502,13 +3499,13 @@ (define-public metabat
(add-after 'unpack 'fix-scons
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "SConstruct"
(("^htslib_dir = 'samtools'")
(string-append "hitslib_dir = '"
(("^htslib_dir += 'samtools'")
(string-append "htslib_dir = '"
(assoc-ref inputs "htslib")
"'"))
(("^samtools_dir = 'samtools'")
(string-append "samtools_dir = '"
(assoc-ref inputs "htslib")
(assoc-ref inputs "samtools")
"'"))
(("^findStaticOrShared\\('bam', hts_lib")
(string-append "findStaticOrShared('bam', '"
@ -3550,7 +3547,7 @@ (define-public metabat
an automated metagenome binning software, which integrates empirical
probabilistic distances of genome abundance and tetranucleotide frequency.")
(license (license:non-copyleft "file://license.txt"
"See license.txt in the distribution.")))))
"See license.txt in the distribution."))))
(define-public minced
(package

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@ -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