* [PATCH] Add Piranha.
@ 2016-04-26 14:09 Ricardo Wurmus
2016-04-27 12:30 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2016-04-26 14:09 UTC (permalink / raw)
To: guix-devel@gnu.org
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From 8ebcd50666e13407d2b74907c9bc5e37ee420192 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 26 Apr 2016 16:08:47 +0200
Subject: [PATCH] gnu: Add Piranha.
* gnu/packages/bioinformatics.scm (piranha): New variable.
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35c3334..7a93c72 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5209,6 +5209,68 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public piranha
+ (package
+ (name "piranha")
+ (version "1.1.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/smithlabcode/piranha"
+ "/archive/svn/tags/piranha-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'copy-smithlab-cpp
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir "src/smithlab_cpp")
+ (for-each (lambda (file)
+ (copy-file file
+ (string-append "./src/smithlab_cpp/"
+ (basename file))))
+ (find-files (assoc-ref inputs "smithlab-cpp")))
+ #t))
+ (add-after 'install 'install-to-store
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))
+ #:configure-flags
+ (list (string-append "--with-bam_tools_headers="
+ (assoc-ref %build-inputs "bamtools") "/include/bamtools")
+ (string-append "--with-bam_tools_library="
+ (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
+ (inputs
+ `(("bamtools" ,bamtools)
+ ("samtools" ,samtools-0.1)
+ ("gsl" ,gsl)
+ ("smithlab-cpp"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (commit "3723e2d")))
+ (file-name "smithlab_cpp-3723e2d-checkout")
+ (sha256
+ (base32
+ "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (home-page "https://github.com/smithlabcode/piranha")
+ (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
+ (description
+ "Piranha is a peak-caller for CLIP-seq and RIP-seq data.")
+ (license license:gpl3+)))
+
(define-public pepr
(package
(name "pepr")
--
2.7.3
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Add Piranha.
2016-04-26 14:09 [PATCH] Add Piranha Ricardo Wurmus
@ 2016-04-27 12:30 ` Ludovic Courtès
2016-05-19 9:27 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2016-04-27 12:30 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel@gnu.org
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 8ebcd50666e13407d2b74907c9bc5e37ee420192 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 26 Apr 2016 16:08:47 +0200
> Subject: [PATCH] gnu: Add Piranha.
>
> * gnu/packages/bioinformatics.scm (piranha): New variable.
[...]
> + (add-after 'unpack 'copy-smithlab-cpp
> + (lambda* (#:key inputs #:allow-other-keys)
> + (mkdir "src/smithlab_cpp")
> + (for-each (lambda (file)
> + (copy-file file
> + (string-append "./src/smithlab_cpp/"
> + (basename file))))
Rather:
(install-file file "src/smithlab_cpp")
> + ,(origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/smithlabcode/smithlab_cpp.git")
> + (commit "3723e2d")))
> + (file-name "smithlab_cpp-3723e2d-checkout")
Either remove the commit ID from ‘file-name’ or introduce a ‘commit’
variable to avoid repetition.
> + (home-page "https://github.com/smithlabcode/piranha")
> + (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
> + (description
> + "Piranha is a peak-caller for CLIP-seq and RIP-seq data.")
Could you expound a bit (info "(guix) Synopses and Descriptions")? :-)
OK with these changes.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Add Piranha.
2016-04-27 12:30 ` Ludovic Courtès
@ 2016-05-19 9:27 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2016-05-19 9:27 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel@gnu.org
Ludovic Courtès <ludo@gnu.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From 8ebcd50666e13407d2b74907c9bc5e37ee420192 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 26 Apr 2016 16:08:47 +0200
>> Subject: [PATCH] gnu: Add Piranha.
>>
>> * gnu/packages/bioinformatics.scm (piranha): New variable.
>
> [...]
>
>> + (add-after 'unpack 'copy-smithlab-cpp
>> + (lambda* (#:key inputs #:allow-other-keys)
>> + (mkdir "src/smithlab_cpp")
>> + (for-each (lambda (file)
>> + (copy-file file
>> + (string-append "./src/smithlab_cpp/"
>> + (basename file))))
>
> Rather:
>
> (install-file file "src/smithlab_cpp")
>
>> + ,(origin
>> + (method git-fetch)
>> + (uri (git-reference
>> + (url "https://github.com/smithlabcode/smithlab_cpp.git")
>> + (commit "3723e2d")))
>> + (file-name "smithlab_cpp-3723e2d-checkout")
>
> Either remove the commit ID from ‘file-name’ or introduce a ‘commit’
> variable to avoid repetition.
>
>> + (home-page "https://github.com/smithlabcode/piranha")
>> + (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
>> + (description
>> + "Piranha is a peak-caller for CLIP-seq and RIP-seq data.")
>
> Could you expound a bit (info "(guix) Synopses and Descriptions")? :-)
>
> OK with these changes.
Thanks for the review. I fixed the patch according to your suggestions
and pushed to master.
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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2016-04-26 14:09 [PATCH] Add Piranha Ricardo Wurmus
2016-04-27 12:30 ` Ludovic Courtès
2016-05-19 9:27 ` Ricardo Wurmus
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