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gnu: metabat: Update to 0.26.3. 

* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
This commit is contained in:
Ben Woodcroft 2016-06-28 21:28:06 +10:00
parent af45244e36
commit 45469ebe52
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1 changed files with 30 additions and 27 deletions
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gnu/packages/bioinformatics.scm
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@ -2486,7 +2486,7 @@ sequences).")
(define-public metabat (define-public metabat
(package (package
(name "metabat") (name "metabat")
(version "0.26.1") (version "0.26.3")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -2495,31 +2495,40 @@ sequences).")
(file-name (string-append name "-" version ".tar.bz2")) (file-name (string-append name "-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa")))) "1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'fix-includes (add-after 'unpack 'fix-includes
(lambda _ (lambda _
(substitute* "SConstruct" (substitute* "src/BamUtils.h"
(("/include/bam/bam.h") (("^#include \"bam/bam\\.h\"")
"/include/samtools/bam.h")) "#include \"samtools/bam.h\"")
(substitute* "src/BamUtils.h" (("^#include \"bam/sam\\.h\"")
(("^#include \"bam/bam\\.h\"") "#include \"samtools/sam.h\""))
"#include \"samtools/bam.h\"") (substitute* "src/KseqReader.h"
(("^#include \"bam/sam\\.h\"") (("^#include \"bam/kseq\\.h\"")
"#include \"samtools/sam.h\"")) "#include \"htslib/kseq.h\""))
(substitute* "src/KseqReader.h" #t))
(("^#include \"bam/kseq\\.h\"")
"#include \"samtools/kseq.h\""))
#t))
(add-after 'unpack 'fix-scons (add-after 'unpack 'fix-scons
(lambda _ (lambda* (#:key inputs #:allow-other-keys)
(substitute* "SConstruct" ; Do not distribute README (substitute* "SConstruct"
(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") (("^htslib_dir = 'samtools'")
"")) (string-append "hitslib_dir = '"
#t)) (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) (delete 'configure)
(replace 'build (replace 'build
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
@ -2528,17 +2537,11 @@ sequences).")
(string-append (string-append
"PREFIX=" "PREFIX="
(assoc-ref outputs "out")) (assoc-ref outputs "out"))
(string-append
"HTSLIB_DIR="
(assoc-ref inputs "htslib"))
(string-append
"SAMTOOLS_DIR="
(assoc-ref inputs "samtools"))
(string-append (string-append
"BOOST_ROOT=" "BOOST_ROOT="
(assoc-ref inputs "boost")) (assoc-ref inputs "boost"))
"install")))) "install"))))
;; check and install carried out during build phase ;; Check and install are carried out during build phase.
(delete 'check) (delete 'check)
(delete 'install)))) (delete 'install))))
(inputs (inputs