On 17/01/16 14:29, Eric Bavier wrote:
On Sun, 17 Jan 2016 11:30:03 +1000
Ben Woodcroft <b.woodcr...@uq.edu.au> wrote:
There is a somewhat popular bioinformatics program muscle whose download
tgz is a tar bomb. The bomb moniker seems especially appropriate here,
since it made the gnu-build-system error out, and patching
gnu-build-system requires a lot of rebuilding. In the attached patches I
fixed gnu-build-system so that the "chdir" is omitted when there is no
directory to chdir into, and then added muscle itself.
See https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00165.html
I think it might be what you're looking for.
Now that url-fetch/tarbomb is available for general use, I've updated
this patch and added a trivial test case. Thanks in advance for review.
ben
>From 014be68f9e82847761f47f0363fa106bf708f14c Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 16 Jan 2016 22:12:23 +1000
Subject: [PATCH] gnu: Add muscle.
* gnu/packages/bioinformatics.scm (muscle): New variable.
---
gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 899ce1c..6e51dde 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2548,6 +2548,40 @@ RNA-Seq, the MISO model uses Bayesian inference to compute the probability
that a read originated from a particular isoform.")
(license license:gpl2)))
+(define-public muscle
+ (package
+ (name "muscle")
+ (version "3.8.1551")
+ (source (origin
+ (method url-fetch/tarbomb)
+ (file-name (string-append name "-" version ".tar.gz"))
+ (uri (string-append
+ "http://www.drive5.com/muscle/muscle_src_";
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags (list "LDLIBS = -lm")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check
+ ;; There are no tests, so just test if it runs.
+ (lambda _ (zero? (system* "./muscle" "-version"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (install-file "muscle" bin)))))))
+ (home-page "http://www.drive5.com/muscle";)
+ (synopsis "Multiple sequence alignment program")
+ (description
+ "MUSCLE aims to be a fast and accurate multiple sequence alignment
+program for nucleotide and protein sequences.")
+ (license license:public-domain)))
+
(define-public orfm
(package
(name "orfm")
--
2.6.3
