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authorBen Woodcroft <donttrustben@gmail.com>2016-06-28 21:28:06 +1000
committerBen Woodcroft <donttrustben@gmail.com>2016-06-28 21:28:06 +1000
commit45469ebe528df81e6c3a7b4aa5a42f914dc28acd (patch)
treec4a4019404a0ade3681d452257db6e12bbc85e8f
parentaf45244e3662d324f37923c7fa120e49673b3ad2 (diff)
downloadpatches-45469ebe528df81e6c3a7b4aa5a42f914dc28acd.tar
patches-45469ebe528df81e6c3a7b4aa5a42f914dc28acd.tar.gz
gnu: metabat: Update to 0.26.3.
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3. [arguments]: Update include and linking paths accordingly.
-rw-r--r--gnu/packages/bioinformatics.scm57
1 files changed, 30 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7ae3593181..fa0979bcea 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2486,7 +2486,7 @@ sequences).")
(define-public metabat
(package
(name "metabat")
- (version "0.26.1")
+ (version "0.26.3")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2495,31 +2495,40 @@ sequences).")
(file-name (string-append name "-" version ".tar.bz2"))
(sha256
(base32
- "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
+ "1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-includes
- (lambda _
- (substitute* "SConstruct"
- (("/include/bam/bam.h")
- "/include/samtools/bam.h"))
- (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 \"samtools/kseq.h\""))
- #t))
+ (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\""))
+ #t))
(add-after 'unpack 'fix-scons
- (lambda _
- (substitute* "SConstruct" ; Do not distribute README
- (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)")
- ""))
- #t))
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "SConstruct"
+ (("^htslib_dir = 'samtools'")
+ (string-append "hitslib_dir = '"
+ (assoc-ref inputs "htslib")
+ "'"))
+ (("^samtools_dir = 'samtools'")
+ (string-append "samtools_dir = '"
+ (assoc-ref inputs "htslib")
+ "'"))
+ (("^findStaticOrShared\\('bam', hts_lib")
+ (string-append "findStaticOrShared('bam', '"
+ (assoc-ref inputs "samtools")
+ "/lib'"))
+ ;; Do not distribute README.
+ (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
+ #t))
(delete 'configure)
(replace 'build
(lambda* (#:key inputs outputs #:allow-other-keys)
@@ -2529,16 +2538,10 @@ sequences).")
"PREFIX="
(assoc-ref outputs "out"))
(string-append
- "HTSLIB_DIR="
- (assoc-ref inputs "htslib"))
- (string-append
- "SAMTOOLS_DIR="
- (assoc-ref inputs "samtools"))
- (string-append
"BOOST_ROOT="
(assoc-ref inputs "boost"))
"install"))))
- ;; check and install carried out during build phase
+ ;; Check and install are carried out during build phase.
(delete 'check)
(delete 'install))))
(inputs