[PATCH] gnu: Add GRIT.

[PATCH] gnu: Add GRIT.

[Ricardo Wurmus]

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From 9d27d88602fe575e0ebf2c0c7841e8aed7aa563c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 10 Apr 2015 11:05:45 +0200
Subject: [PATCH] gnu: Add GRIT.

* gnu/packages/bioinformatics.scm (grit): New variable.
---
 gnu/packages/bioinformatics.scm | 49 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b5eccf..d7f6a0f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -511,6 +511,55 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
     (license license:gpl3)))
 
+(define-public grit
+  (package
+    (name "grit")
+    (version "2.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/nboley/grit/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (alist-cons-after
+        'unpack 'generate-from-cython-sources
+        (lambda* (#:key inputs outputs #:allow-other-keys)
+          (delete-file "grit/sparsify_support_fns.c")
+          (delete-file "grit/call_peaks_support_fns.c")
+          (substitute* "setup.py"
+            (("Cython.Setup") "Cython.Build")
+            (("pyx\", \\]")
+             (string-append "pyx\", ], include_dirs = ['"
+                            (assoc-ref inputs "python-numpy")
+                            "/lib/python2.7/site-packages/numpy/core/include/"
+                            "']"))) #t)
+        %standard-phases)))
+    (inputs
+     `(("python-scipy" ,python2-scipy)
+       ("python-numpy" ,python2-numpy)
+       ("python-pysam" ,python2-pysam)
+       ("python-networkx" ,python2-networkx)))
+    (native-inputs
+     `(("python-cython" ,python2-cython)
+       ("python-setuptools" ,python2-setuptools)))
+    (home-page "http://grit-bio.org")
+    (synopsis "Tool for integrative analysis of RNA-seq type assays")
+    (description
+     "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
+full length transcript models.  When none of these data sources are available,
+GRIT can be run by providing a candidate set of TES or TSS sites.  In
+addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
+also be run in quantification mode, where it uses a provided GTF file and just
+estimates transcript expression.")
+    (license license:gpl3+)))
+
 (define-public hisat
   (package
     (name "hisat")
-- 
2.1.0

Re: [PATCH] gnu: Add GRIT.

[David Thompson]

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

> From 9d27d88602fe575e0ebf2c0c7841e8aed7aa563c Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 10 Apr 2015 11:05:45 +0200
> Subject: [PATCH] gnu: Add GRIT.
>
> * gnu/packages/bioinformatics.scm (grit): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 49 +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 49 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 0b5eccf..d7f6a0f 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -511,6 +511,55 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
>  Illumina, Roche 454, and the SOLiD platform.")
>      (license license:gpl3)))
>  
> +(define-public grit
> +  (package
> +    (name "grit")
> +    (version "2.0.2")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append
> +                    "https://github.com/nboley/grit/archive/"
> +                    version ".tar.gz"))
> +              (file-name (string-append name "-" version ".tar.gz"))
> +              (sha256
> +               (base32
> +                "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:python ,python-2
> +       #:phases
> +       (alist-cons-after
> +        'unpack 'generate-from-cython-sources
> +        (lambda* (#:key inputs outputs #:allow-other-keys)
> +          (delete-file "grit/sparsify_support_fns.c")
> +          (delete-file "grit/call_peaks_support_fns.c")

A comment explaining why these are deleted would be nice.

> +          (substitute* "setup.py"
> +            (("Cython.Setup") "Cython.Build")
> +            (("pyx\", \\]")
> +             (string-append "pyx\", ], include_dirs = ['"
> +                            (assoc-ref inputs "python-numpy")
> +                            "/lib/python2.7/site-packages/numpy/core/include/"
> +                            "']"))) #t)

A comment for this, too, please.  I can tell that this is fixing
something related to numpy, but I'm not sure why it needs to be done.

> +        %standard-phases)))
> +    (inputs
> +     `(("python-scipy" ,python2-scipy)
> +       ("python-numpy" ,python2-numpy)
> +       ("python-pysam" ,python2-pysam)
> +       ("python-networkx" ,python2-networkx)))
> +    (native-inputs
> +     `(("python-cython" ,python2-cython)
> +       ("python-setuptools" ,python2-setuptools)))
> +    (home-page "http://grit-bio.org")
> +    (synopsis "Tool for integrative analysis of RNA-seq type assays")
> +    (description
> +     "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
> +full length transcript models.  When none of these data sources are available,
> +GRIT can be run by providing a candidate set of TES or TSS sites.  In
> +addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
> +also be run in quantification mode, where it uses a provided GTF file and just
> +estimates transcript expression.")
> +    (license license:gpl3+)))
> +
>  (define-public hisat
>    (package
>      (name "hisat")
> -- 
> 2.1.0
>
>

Looks good otherwise.  Thanks!

-- 
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate

Re: [PATCH] gnu: Add GRIT.

[Ludovic Courtès]

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

> From 9d27d88602fe575e0ebf2c0c7841e8aed7aa563c Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 10 Apr 2015 11:05:45 +0200
> Subject: [PATCH] gnu: Add GRIT.
>
> * gnu/packages/bioinformatics.scm (grit): New variable.

OK!

Ludo’.