[PATCH] tar bombs and muscle

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

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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 I 
fixed gnu-build-system so that the "chdir" is omitted when there is no 
directory to chdir into, and then added muscle itself.

Is it OK in these rare instances to put the archive contents into the 
directory as-is, or is something more complex like making a directory 
and moving everything there more appropriate?

I imagine it might be best to let this slide into the next core-updates.

Thanks,
ben

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From 9400f88a9f70d47f1e835a98842b894e640d0e4a 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 a905ccf..4a7a2c2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2176,6 +2176,37 @@ the ability to go from raw sequences to the generation of visualization tools
 to describe ecological α and β diversity measurements.")
     (license license:gpl3)))
 
+(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


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From 9e272374a3531d1df6d36e595dad0b715731e4cd 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