[PATCH] gnu: Add CLIPper.

[PATCH] gnu: Add CLIPper.

[Ricardo Wurmus]

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From 894c295fe9437987ed5d447c3122045a73259bc1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 25 Feb 2015 16:38:17 +0100
Subject: [PATCH] gnu: Add CLIPper.

* gnu/packages/bioinformatics.scm (clipper): New variable.
---
 gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a425f61..b08e133 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -235,6 +235,44 @@ gapped, local, and paired-end alignment modes.")
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public clipper
+  (package
+    (name "clipper")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/YeoLab/clipper/archive/"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
+              (modules '((guix build utils)))
+              (snippet
+               ;; remove unnecessary setup dependency
+               '(substitute* "setup.py"
+                  (("setup_requires = .*") "")))))
+    (build-system python-build-system)
+    (arguments `(#:python ,python-2)) ; only Python 2 is supported
+    (inputs
+     `(("htseq" ,htseq)
+       ("python-pybedtools" ,python2-pybedtools)
+       ("python-cython" ,python2-cython)
+       ("python-scikit-learn" ,python2-scikit-learn)
+       ("python-matplotlib" ,python2-matplotlib)
+       ("python-pysam" ,python2-pysam)
+       ("python-numpy" ,python2-numpy)
+       ("python-scipy" ,python2-scipy)))
+    (native-inputs
+     `(("python-mock" ,python2-mock) ; for tests
+       ("python-pytz" ,python2-pytz) ; for tests
+       ("python-setuptools" ,python2-setuptools)))
+    (home-page "https://github.com/YeoLab/clipper")
+    (synopsis "CLIP peak enrichment recognition")
+    (description
+     "CLIPper is a tool to define peaks in CLIP-seq datasets.")
+    (license license:gpl2)))
+
 (define-public flexbar
   (package
     (name "flexbar")
-- 
2.1.0

Re: [PATCH] gnu: Add CLIPper.

[Andreas Enge]

Okay to push.

Andreas

Re: [PATCH] gnu: Add CLIPper.

[Mark H Weaver]

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

> +(define-public clipper
> +  (package
> +    (name "clipper")
> +    (version "0.3.0")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append
> +                    "https://github.com/YeoLab/clipper/archive/"
> +                    version ".tar.gz"))

For packages where the last component of the source URI (after the last
'/') does not include the name of the package, please add something like
this to the 'origin' specification:

              (file-name (string-append name "-" version ".tar.gz"))

Without this, the name of the source tarball in the store becomes
something like /gnu/store/<HASH>-0.3.0.tar.gz, which is not so good.

In core-updates f586c877054, I fixed as many of these as I could find
(all the github ones anyway), but it seems that we'll have to make
another pass at some point.

In the meantime, could you fix the ones you've recently added that are
not already fixed in f586c877054?

      Thanks!
        Mark