[PATCH] Add bwa.

[PATCH] Add bwa.

[Ricardo Wurmus]

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Hi Guix,

here's a patch for an aligner tool:


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From 6c03af7501c53c06a808906ce7d4fbd431bbf1ba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 12 Mar 2015 12:35:14 +0100
Subject: [PATCH] gnu: Add bwa.

* gnu/packages/bioinformatics.scm (bwa): New variable.
---
 gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 22ce71b..67326aa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -238,6 +238,53 @@ gapped, local, and paired-end alignment modes.")
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public bwa
+  (package
+    (name "bwa")
+    (version "0.7.12")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ;no "check" target
+       #:phases
+       (alist-replace
+        'install
+        (lambda* (#:key outputs #:allow-other-keys)
+          (let ((bin (string-append
+                      (assoc-ref outputs "out") "/bin"))
+                (doc (string-append
+                      (assoc-ref outputs "out") "/share/doc/bwa"))
+                (man (string-append
+                      (assoc-ref outputs "out") "/share/man/man1")))
+            (mkdir-p bin)
+            (mkdir-p doc)
+            (mkdir-p man)
+            (copy-file "bwa" (string-append bin "/bwa"))
+            (copy-file "README.md" (string-append doc "/README.md"))
+            (copy-file "bwa.1" (string-append man "/bwa.1"))))
+        ;; no "configure" script
+        (alist-delete 'configure %standard-phases))))
+    (inputs `(("zlib" ,zlib)))
+    (home-page "http://bio-bwa.sourceforge.net/")
+    (synopsis "Burrows-Wheeler aligner")
+    (description
+     "BWA is a software package for mapping low-divergent sequences against a
+large reference genome, such as the human genome.  It consists of three
+algorithms: BWA-backtrack, BWA-SW and BWA-MEM.  The first algorithm is
+designed for Illumina sequence reads up to 100bp, while the rest two for
+longer sequences ranged from 70bp to 1Mbp.  BWA-MEM and BWA-SW share similar
+features such as long-read support and split alignment, but BWA-MEM, which is
+the latest, is generally recommended for high-quality queries as it is faster
+and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
+70-100bp Illumina reads.")
+    (license license:gpl3)))
+
 (define-public clipper
   (package
     (name "clipper")
-- 
2.1.0


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The license is really just GPLv3; there are no license headers in the
files that would imply otherwise and the only mention of the GPLv3 is in
the README.

~~ Ricardo

Re: [PATCH] Add bwa.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 6c03af7501c53c06a808906ce7d4fbd431bbf1ba Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 12 Mar 2015 12:35:14 +0100
> Subject: [PATCH] gnu: Add bwa.
>
> * gnu/packages/bioinformatics.scm (bwa): New variable.

[...]

> +    (synopsis "Burrows-Wheeler aligner")

s/aligner/genome sequence aligner/ or something like that.

> +    (license license:gpl3)))

GPLv3-only?

Other than that LGTM, thanks!

Ludo’.

Re: [PATCH] Add bwa.

[Ricardo Wurmus]

Ludovic Courtès writes:

>> +    (synopsis "Burrows-Wheeler aligner")
>
> s/aligner/genome sequence aligner/ or something like that.

Is a change to "Burrows-Wheeler sequence aligner" acceptable?  I don't
think "sequence aligner" has any other meaning in this context (and in
combination with "Burrows-Wheeler").

>> +    (license license:gpl3)))
>
> GPLv3-only?

Yes, just GPLv3 as far as I can tell.  The usual upgrade clause is
nowhere to be found in the source tree.

~~ Ricardo

Re: [PATCH] Add bwa.

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> Ludovic Courtès writes:
>
>>> +    (synopsis "Burrows-Wheeler aligner")
>>
>> s/aligner/genome sequence aligner/ or something like that.
>
> Is a change to "Burrows-Wheeler sequence aligner" acceptable?  I don't
> think "sequence aligner" has any other meaning in this context (and in
> combination with "Burrows-Wheeler").

Yes, sounds good.

>>> +    (license license:gpl3)))
>>
>> GPLv3-only?
>
> Yes, just GPLv3 as far as I can tell.  The usual upgrade clause is
> nowhere to be found in the source tree.

If there are no file headers or documents specifying the version, then
it’s effectively GPLv3+ (actually it’s even any version, per Section 14,
but we usually do GPLv3+ in this case.)

Thanks,
Ludo’.