* [PATCH]: gnu: Add STAR.
@ 2015-02-09 14:41 Ricardo Wurmus
2015-02-09 23:08 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-02-09 14:41 UTC (permalink / raw)
To: Guix-devel
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Hi Guix,
here's another aligner for RNA-seq data. The description is rather
dense but that's what I came up with after deleting as much as I could
from the description here:
http://bioinformatics.oxfordjournals.org/content/29/1/15
~~ Ricardo
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From efd3b0fd1b5ed0b7ca0168e3356c950482b694d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 9 Feb 2015 15:38:30 +0100
Subject: [PATCH] gnu: Add STAR.
* gnu/packages/bioinformatics.scm (star): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 425558d..c8fff5f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -31,6 +31,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages tbb)
+ #:use-module (gnu packages vim)
#:use-module (gnu packages zip))
(define-public bedtools
@@ -360,3 +361,50 @@ algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
+
+(define-public star
+ (package
+ (name "star")
+ (version "2.4.0j")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/alexdobin/STAR/archive/STAR_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "source/Makefile"
+ (("/bin/rm") "rm")))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#: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/")))
+ (mkdir-p bin)
+ (copy-file "STAR" (string-append bin "STAR"))))
+ (alist-delete
+ 'configure %standard-phases)))))
+ (native-inputs
+ `(("vim" ,vim))) ; for xxd
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/alexdobin/STAR")
+ (synopsis "Universal RNA-seq aligner")
+ (description
+ "The Spliced Transcripts Alignment to a Reference (STAR) software is
+based on a previously undescribed RNA-seq alignment algorithm that uses
+sequential maximum mappable seed search in uncompressed suffix arrays followed
+by seed clustering and stitching procedure. In addition to unbiased de novo
+detection of canonical junctions, STAR can discover non-canonical splices and
+chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
+sequences.")
+ (license license:gpl3)))
--
2.1.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH]: gnu: Add STAR.
2015-02-09 14:41 [PATCH]: gnu: Add STAR Ricardo Wurmus
@ 2015-02-09 23:08 ` Ludovic Courtès
2015-02-10 9:40 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Ludovic Courtès @ 2015-02-09 23:08 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From efd3b0fd1b5ed0b7ca0168e3356c950482b694d6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 9 Feb 2015 15:38:30 +0100
> Subject: [PATCH] gnu: Add STAR.
>
> * gnu/packages/bioinformatics.scm (star): New variable.
LGTM!
> + (license license:gpl3)))
GPLv3-only?
Thanks,
Ludo'.
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH]: gnu: Add STAR.
2015-02-09 23:08 ` Ludovic Courtès
@ 2015-02-10 9:40 ` Ricardo Wurmus
2015-02-10 12:51 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-02-10 9:40 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: Guix-devel
Ludovic Courtès writes:
>> + (license license:gpl3)))
>
> GPLv3-only?
Actually, searching the source tree shows me that LICENSE includes the
"or (at your option) any later version" phrase; but the included copy of
htslib that is built as part of the STAR aligner is MIT licensed.
I'll update the license field to
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license (list license:gpl3+ license:expat))
Is this appropriate?
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH]: gnu: Add STAR.
2015-02-10 9:40 ` Ricardo Wurmus
@ 2015-02-10 12:51 ` Ludovic Courtès
0 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2015-02-10 12:51 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Ludovic Courtès writes:
>>> + (license license:gpl3)))
>>
>> GPLv3-only?
>
> Actually, searching the source tree shows me that LICENSE includes the
> "or (at your option) any later version" phrase; but the included copy of
> htslib that is built as part of the STAR aligner is MIT licensed.
>
> I'll update the license field to
>
> ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
> (license (list license:gpl3+ license:expat))
>
> Is this appropriate?
Since the combined work is GPLv3+ anyway, I would keep the comment but
set the ‘license’ field to GPL3+.
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
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2015-02-09 14:41 [PATCH]: gnu: Add STAR Ricardo Wurmus
2015-02-09 23:08 ` Ludovic Courtès
2015-02-10 9:40 ` Ricardo Wurmus
2015-02-10 12:51 ` Ludovic Courtès
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