* [PATCH] gnu: Add GRIT.
@ 2015-04-10 9:06 Ricardo Wurmus
2015-04-10 11:05 ` David Thompson
2015-04-10 11:49 ` Ludovic Courtès
0 siblings, 2 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-04-10 9:06 UTC (permalink / raw
To: Guix-devel
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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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add GRIT.
2015-04-10 9:06 [PATCH] gnu: Add GRIT Ricardo Wurmus
@ 2015-04-10 11:05 ` David Thompson
2015-04-10 11:49 ` Ludovic Courtès
1 sibling, 0 replies; 3+ messages in thread
From: David Thompson @ 2015-04-10 11:05 UTC (permalink / raw
To: Ricardo Wurmus, Guix-devel
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
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add GRIT.
2015-04-10 9:06 [PATCH] gnu: Add GRIT Ricardo Wurmus
2015-04-10 11:05 ` David Thompson
@ 2015-04-10 11:49 ` Ludovic Courtès
1 sibling, 0 replies; 3+ messages in thread
From: Ludovic Courtès @ 2015-04-10 11:49 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: Guix-devel
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’.
^ permalink raw reply [flat|nested] 3+ messages in thread
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2015-04-10 9:06 [PATCH] gnu: Add GRIT Ricardo Wurmus
2015-04-10 11:05 ` David Thompson
2015-04-10 11:49 ` Ludovic Courtès
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