[PATCH] Add Piranha.

[PATCH] Add Piranha.

[Ricardo Wurmus]

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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

Re: [PATCH] Add Piranha.

[Ludovic Courtès]

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’.

Re: [PATCH] Add Piranha.

[Ricardo Wurmus]

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