Re: [PATCH] tar bombs and muscle

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

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On 17/01/16 11:30, Ben Woodcroft wrote:
> Hi,
>
> 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
Oops, I wasn't coming off master, so those packages are not apply-able. 
Attached is better.

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From 530d81289ef5cab7010209fe0604a82b73459e4c Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 16 Jan 2016 22:02:22 +1000
Subject: [PATCH 1/2] build: Accept source archives that do not contain a
 directory.

* guix/build/gnu-build-system.scm (unpack): Do not attempt to change
directory after extracting archive if the archive does not contain any
directories.
---
 guix/build/gnu-build-system.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/guix/build/gnu-build-system.scm b/guix/build/gnu-build-system.scm
index ff7646b..f1a84ef 100644
--- a/guix/build/gnu-build-system.scm
+++ b/guix/build/gnu-build-system.scm
@@ -142,7 +142,10 @@ working directory."
       (and (if (string-suffix? ".zip" source)
                (zero? (system* "unzip" source))
                (zero? (system* "tar" "xvf" source)))
-           (chdir (first-subdirectory ".")))))
+           (let ((subdirectory (first-subdirectory ".")))
+             (if subdirectory
+                 (chdir (first-subdirectory "."))
+                 #t)))))
 
 ;; See <http://bugs.gnu.org/17840>.
 (define* (patch-usr-bin-file #:key native-inputs inputs
-- 
2.6.3


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From 567ddebd4f9a8d9e0b5681dae1ec639987c69064 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 16 Jan 2016 22:12:23 +1000
Subject: [PATCH 2/2] gnu: Add muscle.

* gnu/packages/bioinformatics.scm (muscle): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 314d0ad..f9d8068 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2070,6 +2070,37 @@ 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)
+              (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")
+       #:tests? #f ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (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