>From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Tue, 19 Jan 2016 16:04:01 +0100
Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
---
gnu/packages/bioinformatics.scm | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74cadff..d30b0c9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3259,15 +3259,15 @@ of these reads to align data quickly through a hash-based indexing scheme.")
'(#:tests? #f ;no check target
#:make-flags '("STAR")
#:phases
- (alist-cons-after
- 'unpack 'enter-source-dir (lambda _ (chdir "source"))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (install-file "STAR" bin)))
- (alist-delete
- 'configure %standard-phases)))))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-source-dir
+ (lambda _ (chdir "source") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (install-file "STAR" bin))
+ #t))
+ (delete 'configure))))
(native-inputs
`(("vim" ,vim))) ; for xxd
(inputs
--
2.1.0
>From 4efd7a8afe3fbc03f59c1061e9ab2cfcb7c88160 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Tue, 19 Jan 2016 16:26:47 +0100
Subject: [PATCH 2/2] gnu: star: Update to 2.5.0c.
* gnu/packages/bioinformatics.scm (star): Update to 2.5.0c.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++--------
1 file changed, 32 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d30b0c9..20a150f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3241,19 +3241,25 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(define-public star
(package
(name "star")
- (version "2.4.2a")
+ (version "2.5.0c")
(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"))
+ "1hd662ijwns6rpsd5536sm3h69yfb6xsfkrrrlnyh745gf6d5z4q"))
(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
@@ -3262,6 +3268,23 @@ 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/")))
@@ -3271,7 +3294,8 @@ 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
--
2.1.0
