[PATCH] gnu: Add libBigWig.

[PATCH] gnu: Add libBigWig.

[Ricardo Wurmus]

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Hi Guix,

the description is a little short.  Basically, this is a cleaner
reimplementation of a popular tool/library that is released under a
non-commercial license.  There is little more I can say about it and the
original description just references that other tool.

Any ideas how to improve this?

~~ Ricardo


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From d315b3857072fdb0f2f322eaa7562d0bf0c92017 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 24 Feb 2016 17:17:53 +0100
Subject: [PATCH] gnu: Add libBigWig.

* gnu/packages/bioinformatics.scm (libbigwig): New variable.
---
 gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 623eeb6..16cda70 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -40,6 +40,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
@@ -1081,6 +1082,50 @@ preparation protocols.")
 other types of unwanted sequence from high-throughput sequencing reads.")
     (license license:expat)))
 
+(define-public libbigwig
+  (package
+    (name "libbigwig")
+    (version "0.1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/dpryan79/libBigWig/"
+                                  "archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'check 'disable-curl-test
+           (lambda _
+             (substitute* "Makefile"
+               (("./test/testRemote.*") ""))
+             #t))
+         (add-before 'install 'create-target-dirs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p (string-append out "/lib"))
+               (mkdir-p (string-append out "/include"))
+               #t))))))
+    (inputs
+     `(("zlib" ,zlib)
+       ("curl" ,curl)))
+    (native-inputs
+     `(("doxygen" ,doxygen)))
+    (home-page "https://github.com/dpryan79/libBigWig")
+    (synopsis "C library for handling bigWig files")
+    (description
+     "This package provides a C library for parsing local and remote BigWig
+files.")
+    (license license:expat)))
+
 (define-public deeptools
   (package
     (name "deeptools")
-- 
2.1.0

Re: [PATCH] gnu: Add libBigWig.

[Leo Famulari]

On Wed, Feb 24, 2016 at 05:21:47PM +0100, Ricardo Wurmus wrote:
> Hi Guix,
> 
> the description is a little short.  Basically, this is a cleaner
> reimplementation of a popular tool/library that is released under a
> non-commercial license.  There is little more I can say about it and the
> original description just references that other tool.
> 
> Any ideas how to improve this?

If you think it will be clear to the intended audience, I'd say it's
fine.

If "Kent's library" is well-known in the field, would it make sense to
refer to it?

> +         (add-before 'install 'create-target-dirs
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let ((out (assoc-ref outputs "out")))
> +               (mkdir-p (string-append out "/lib"))
> +               (mkdir-p (string-append out "/include"))
> +               #t))))))

Does it make sense to upstream this? I understand if it's not worth your
time...

Re: [PATCH] gnu: Add libBigWig.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Wed, Feb 24, 2016 at 05:21:47PM +0100, Ricardo Wurmus wrote:
>> Hi Guix,
>> 
>> the description is a little short.  Basically, this is a cleaner
>> reimplementation of a popular tool/library that is released under a
>> non-commercial license.  There is little more I can say about it and the
>> original description just references that other tool.
>> 
>> Any ideas how to improve this?
>
> If you think it will be clear to the intended audience, I'd say it's
> fine.

Okay.

> If "Kent's library" is well-known in the field, would it make sense to
> refer to it?

I don’t know.  They refer to the kentUtils, but I don’t really want to
mention them.  They are a grab bag with many different features (only
one of which is reading bigwig files), so I don’t think it would clarify
much.

>> +         (add-before 'install 'create-target-dirs
>> +           (lambda* (#:key outputs #:allow-other-keys)
>> +             (let ((out (assoc-ref outputs "out")))
>> +               (mkdir-p (string-append out "/lib"))
>> +               (mkdir-p (string-append out "/include"))
>> +               #t))))))
>
> Does it make sense to upstream this? I understand if it's not worth your
> time...

Done:

  https://github.com/dpryan79/libBigWig/issues/6

A new commit has already been made but there’s no release with that
change yet.  I’ll add a comment to this phase.

Thanks for taking the time to review this patch!

~~ Ricardo

Re: [PATCH] gnu: Add libBigWig.

[Leo Famulari]

On Thu, Feb 25, 2016 at 11:37:38AM +0100, Ricardo Wurmus wrote:
> 
> Leo Famulari <leo@famulari.name> writes:
> 
> > On Wed, Feb 24, 2016 at 05:21:47PM +0100, Ricardo Wurmus wrote:
> >> Hi Guix,
> >> 
> >> the description is a little short.  Basically, this is a cleaner
> >> reimplementation of a popular tool/library that is released under a
> >> non-commercial license.  There is little more I can say about it and the
> >> original description just references that other tool.
> >> 
> >> Any ideas how to improve this?
> >
> > If you think it will be clear to the intended audience, I'd say it's
> > fine.
> 
> Okay.
> 
> > If "Kent's library" is well-known in the field, would it make sense to
> > refer to it?
> 
> I don’t know.  They refer to the kentUtils, but I don’t really want to
> mention them.  They are a grab bag with many different features (only
> one of which is reading bigwig files), so I don’t think it would clarify
> much.
> 
> >> +         (add-before 'install 'create-target-dirs
> >> +           (lambda* (#:key outputs #:allow-other-keys)
> >> +             (let ((out (assoc-ref outputs "out")))
> >> +               (mkdir-p (string-append out "/lib"))
> >> +               (mkdir-p (string-append out "/include"))
> >> +               #t))))))
> >
> > Does it make sense to upstream this? I understand if it's not worth your
> > time...
> 
> Done:
> 
>   https://github.com/dpryan79/libBigWig/issues/6
> 
> A new commit has already been made but there’s no release with that
> change yet.  I’ll add a comment to this phase.

That's awesome, thank you!

> 
> Thanks for taking the time to review this patch!
> 
> ~~ Ricardo