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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-19 16:26:47 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-23 08:40:14 +0100 |
| commit | 3062d750b4f8e16c979629360bf2dc411b71b04c (patch) | |
| tree | 9fafcf49e74e36adf2557426c190d49f6501268c /gnu | |
| parent | c0266e8d031852931d1cc324dd56cf075cecc9a2 (diff) | |
| download | patches-3062d750b4f8e16c979629360bf2dc411b71b04c.tar patches-3062d750b4f8e16c979629360bf2dc411b71b04c.tar.gz | |
gnu: star: Update to 2.5.1b.
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 32 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 485faefdc9..fa2bea732c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3019,19 +3019,25 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public star (package (name "star") - (version "2.4.2a") + (version "2.5.1b") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/alexdobin/STAR/archive/STAR_" - version ".tar.gz")) + (uri (string-append "https://github.com/alexdobin/STAR/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc")) + "0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4")) (modules '((guix build utils))) (snippet - '(substitute* "source/Makefile" - (("/bin/rm") "rm"))))) + '(begin + (substitute* "source/Makefile" + (("/bin/rm") "rm")) + ;; Remove pre-built binaries and bundled htslib sources. + (delete-file-recursively "bin/MacOSX_x86_64") + (delete-file-recursively "bin/Linux_x86_64") + (delete-file-recursively "source/htslib") + #t)))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no check target @@ -3040,6 +3046,23 @@ of these reads to align data quickly through a hash-based indexing scheme.") (modify-phases %standard-phases (add-after 'unpack 'enter-source-dir (lambda _ (chdir "source") #t)) + (add-after 'enter-source-dir 'do-not-use-bundled-htslib + (lambda _ + (substitute* "Makefile" + (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" + _ prefix) prefix)) + (substitute* '("BAMfunctions.cpp" + "signalFromBAM.h" + "bam_cat.h" + "bam_cat.c" + "STAR.cpp" + "bamRemoveDuplicates.cpp") + (("#include \"htslib/([^\"]+\\.h)\"" _ header) + (string-append "#include <" header ">"))) + (substitute* "IncludeDefine.h" + (("\"htslib/(htslib/[^\"]+.h)\"" _ header) + (string-append "<" header ">"))) + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) @@ -3049,7 +3072,8 @@ of these reads to align data quickly through a hash-based indexing scheme.") (native-inputs `(("vim" ,vim))) ; for xxd (inputs - `(("zlib" ,zlib))) + `(("htslib" ,htslib) + ("zlib" ,zlib))) (home-page "https://github.com/alexdobin/STAR") (synopsis "Universal RNA-seq aligner") (description |