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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-19 16:26:47 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-23 08:40:14 +0100
commit3062d750b4f8e16c979629360bf2dc411b71b04c (patch)
tree9fafcf49e74e36adf2557426c190d49f6501268c
parentc0266e8d031852931d1cc324dd56cf075cecc9a2 (diff)
downloadguix-3062d750b4f8e16c979629360bf2dc411b71b04c.tar
guix-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".
-rw-r--r--gnu/packages/bioinformatics.scm40
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