From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: bug? also [PATCH] Add snap-aligner.
Date: Thu, 10 Dec 2015 21:33:42 +1000 [thread overview]
Message-ID: <56696316.20402@uq.edu.au> (raw)
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Hey,
I tried doing the check for reproducibility
$ ./pre-inst-env guix build --rounds=3 snap-aligner
but it only built once.
$ ./pre-inst-env guix build --check snap-aligner
;;; note: source file /home/ben/git/guix/gnu/packages/bioinformatics.scm
;;; newer than compiled
/home/ben/git/guix/gnu/packages/bioinformatics.go
guix build: error: build failed: unsupported build mode
Did I mess that up?
Thanks,
ben
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From 6dd854282c75c30b8ae8eb922a2bc65a5be599c0 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 10 Dec 2015 20:56:52 +1000
Subject: [PATCH] gnu: Add snap-aligner.
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35cec1e..836b4fa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2792,6 +2792,44 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
(license license:gpl3)))
+(define-public snap-aligner
+ (package
+ (name "snap-aligner")
+ (version "1.0beta.18")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/amplab/snap/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))
+ (file-name (string-append name "-" version ".tar.gz"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (copy-file "snap-aligner"
+ (string-append bin "/snap-aligner"))
+ (copy-file "SNAPCommand"
+ (string-append bin "/SNAPCommand"))))))))
+ (native-inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://snap.cs.berkeley.edu/")
+ (synopsis "Short read DNA sequence aligner")
+ (description
+ "SNAP is a fast and accurate aligner for short DNA reads. It is
+optimized for modern read lengths of 100 bases or higher, and takes advantage
+of these reads to align data quickly through a hash-based indexing scheme.")
+ (license license:asl2.0)))
+
(define-public star
(package
(name "star")
--
2.5.0
next reply other threads:[~2015-12-10 11:33 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-12-10 11:33 Ben Woodcroft [this message]
2015-12-10 15:54 ` bug? also [PATCH] Add snap-aligner Ricardo Wurmus
2015-12-10 23:41 ` Ben Woodcroft
2015-12-11 13:35 ` Ricardo Wurmus
2015-12-11 9:39 ` Ludovic Courtès
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