Re: [PATCH] tar bombs and muscle

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

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On 17/01/16 14:29, Eric Bavier wrote:
> On Sun, 17 Jan 2016 11:30:03 +1000
> Ben Woodcroft <b.woodcroft@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

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From 014be68f9e82847761f47f0363fa106bf708f14c Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@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