[PATCH] Add pyicoteo.

[PATCH] Add pyicoteo.

[Ricardo Wurmus]

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From f92a3c18613945df3e5fcf6009f8f329da06ebb9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 11 Mar 2016 17:01:00 +0100
Subject: [PATCH] gnu: Add pyicoteo.

* gnu/packages/bioinformatics.scm (pyicoteo): 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 2f0d2db..2566a36 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2622,6 +2622,44 @@ the phenotype as it models the data.")
 generated using the PacBio Iso-Seq protocol.")
       (license license:bsd-3))))
 
+(define-public pyicoteo
+  (package
+    (name "pyicoteo")
+    (version "2.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
+                           "pyicoteo/get/v" version ".tar.bz2"))
+       (file-name (string-append name "-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; does not work with Python 3 
+       #:tests? #f))      ; there are no tests
+    (inputs
+     `(("python2-matplotlib" ,python2-matplotlib)))
+    (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
+    (synopsis "Analyze high-throughput genetic sequencing data")
+    (description
+     "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
+sequencing data.  It works with genomic coordinates.  There are currently six
+different command-line tools:
+
+@enumerate
+@item pyicoregion: for generating exploratory regions automatically;
+@item pyicoenrich: for differential enrichment between two conditions;
+@item pyicoclip: for calling CLIP-Seq peaks without a control;
+@item pyicos: for genomic coordinates manipulation;
+@item pyicoller: for peak calling on punctuated ChIP-Seq;
+@item pyicount: to count how many reads from N experiment files overlap in a
+  region file;
+@item pyicotrocol: to combine operations from pyicoteo.
+@end enumerate\n")
+    (license license:gpl3+)))
+
 (define-public prodigal
   (package
     (name "prodigal")
-- 
2.1.0

Re: [PATCH] Add pyicoteo.

[Ricardo Wurmus]

Sorry, there was a trailing white-space character.  I updated this
locally but won’t resend the patch.

~~ Ricardo

Re: [PATCH] Add pyicoteo.

[Ludovic Courtès]

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

> From f92a3c18613945df3e5fcf6009f8f329da06ebb9 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 11 Mar 2016 17:01:00 +0100
> Subject: [PATCH] gnu: Add pyicoteo.
>
> * gnu/packages/bioinformatics.scm (pyicoteo): New variable.

LGTM, thanks!

Ludo'.

Re: [PATCH] Add pyicoteo.

[Jean Louis]

Hello,

Please, if someone can add patches for following programs:

http://wmbiff.sourceforge.net/ - WMBiff for WindowMaker,
very useful tool to know when emails arrive

IceWm: http://www.icewm.org/ -- I prefer something like:
https://github.com/bbidulock/icewm branch which is
maintained -- it is very fast and user friendly Window
Manager

PDMenu: https://joeyh.name/code/pdmenu/ for menus, beautiful
shell menus, to read emails, see mail queue, whatever
someone likes, although I would rather like to have that in
Guile.

And most important, really nice MTA:
http://www.courier-mta.org/

And new version of PostgreSQL:
http://www.postgresql.org/

Very fast Perl templating engine:
https://metacpan.org/pod/Text::NeatTemplate

And I would like to offer dollars or euros for above
packages to be added to Guix. Because now I don't have new
laptop, cannot break Debian to install Guix, but must use
Guix, and I am sending thousands of emails per day, by using
the above stuff. So per package €10 is alright for me. I
guess there is nothing wrong to pay for the works.

Jean Louis

On Fri, Mar 11, 2016 at 05:29:08PM +0100, Ludovic Courtès wrote:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> 
> > From f92a3c18613945df3e5fcf6009f8f329da06ebb9 Mon Sep 17 00:00:00 2001
> > From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> > Date: Fri, 11 Mar 2016 17:01:00 +0100
> > Subject: [PATCH] gnu: Add pyicoteo.
> >
> > * gnu/packages/bioinformatics.scm (pyicoteo): New variable.
> 
> LGTM, thanks!
> 
> Ludo'.
>