[PATCH] Add cutadapt.

[PATCH] Add cutadapt.

[Ricardo Wurmus]

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From 18a14112b6e22248638d2b34e1c1b935e1bcd343 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Mar 2015 16:17:55 +0100
Subject: [PATCH] gnu: Add cutadapt.

* gnu/packages/bioinformatics.scm (cutadapt): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46ce4f4..5805e42 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19,6 +19,7 @@
 (define-module (gnu packages bioinformatics)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
@@ -405,6 +406,45 @@ files between different genome assemblies.  It supports most commonly used
 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
     (license license:gpl2+)))
 
+(define-public cutadapt
+  (package
+    (name "cutadapt")
+    (version "1.8")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/marcelm/cutadapt/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
+    (build-system python-build-system)
+    (arguments
+     ;; tests must be run after install
+     `(#:phases (alist-cons-after
+                 'install 'check
+                 (lambda* (#:key outputs #:allow-other-keys)
+                   (setenv "PYTHONPATH"
+                           (string-append
+                            (getenv "PYTHONPATH")
+                            ":" (assoc-ref outputs "out")
+                            "/lib/python"
+                            ,(version-major+minor (package-version python))
+                            "/site-packages"))
+                   (zero? (system* "nosetests" "-P" "tests")))
+                 (alist-delete 'check %standard-phases))))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-nose" ,python-nose)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "https://code.google.com/p/cutadapt/")
+    (synopsis "Remove adapter sequences from nucleotide sequencing reads")
+    (description
+     "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
+other types of unwanted sequence from high-throughput sequencing reads.")
+    (license license:expat)))
+
 (define-public flexbar
   (package
     (name "flexbar")
-- 
2.1.0

Re: [PATCH] Add cutadapt.

[Ludovic Courtès]

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

> From 18a14112b6e22248638d2b34e1c1b935e1bcd343 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Mar 2015 16:17:55 +0100
> Subject: [PATCH] gnu: Add cutadapt.
>
> * gnu/packages/bioinformatics.scm (cutadapt): New variable.

[...]

> +                   (setenv "PYTHONPATH"
> +                           (string-append
> +                            (getenv "PYTHONPATH")
> +                            ":" (assoc-ref outputs "out")
> +                            "/lib/python"
> +                            ,(version-major+minor (package-version python))
> +                            "/site-packages"))

It’s best to check the Python version on the build side, using something
like ‘get-python-version’ from python-build-system.scm (so that if
someone inherits this package and changes the Python that is used it
still works.)

Other than that LGTM!

Ludo’.

Re: [PATCH] Add cutadapt.

[Ricardo Wurmus]

Ludovic Courtès writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From 18a14112b6e22248638d2b34e1c1b935e1bcd343 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Fri, 20 Mar 2015 16:17:55 +0100
>> Subject: [PATCH] gnu: Add cutadapt.
>>
>> * gnu/packages/bioinformatics.scm (cutadapt): New variable.
>
> [...]
>
>> +                   (setenv "PYTHONPATH"
>> +                           (string-append
>> +                            (getenv "PYTHONPATH")
>> +                            ":" (assoc-ref outputs "out")
>> +                            "/lib/python"
>> +                            ,(version-major+minor (package-version python))
>> +                            "/site-packages"))
>
> It’s best to check the Python version on the build side, using something
> like ‘get-python-version’ from python-build-system.scm (so that if
> someone inherits this package and changes the Python that is used it
> still works.)

I made this change and pushed the patch just now.
Thanks for the review!

~~ Ricardo