[PATCH] gnu: Add r-centipede.

[PATCH] gnu: Add r-centipede.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (r-centipede): New variable.
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7d025ef..d7957cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -441,6 +441,27 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public r-centipede
+  (package
+    (name "r-centipede")
+    (version "1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://download.r-forge.r-project.org/"
+                                  "src/contrib/CENTIPEDE_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
+    (build-system r-build-system)
+    (home-page "http://centipede.uchicago.edu/")
+    (synopsis "Predict transcription factor binding sites")
+    (description
+     "Centipede fits a bayesian hierarchical mixture model to learn
+transcription-factor-specific distribution of experimental data on a
+particular cell-type for a set of candidate binding sites described by a
+genetic motif.")
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public bioperl-minimal
   (let* ((inputs `(("perl-module-build" ,perl-module-build)
                    ("perl-data-stag" ,perl-data-stag)
-- 
2.7.3

Re: [PATCH] gnu: Add r-centipede.

[Leo Famulari]

On Mon, May 02, 2016 at 04:49:21PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-centipede): New variable.

> +    (synopsis "Predict transcription factor binding sites")

And here I thought it would be a centipede genome ;)

> +    (license (list license:gpl2+ license:gpl3+))))

If something is gpl2+, can it also be gpl3+? I'm not sure, just asking
for clarification.

Re: [PATCH] gnu: Add r-centipede.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Mon, May 02, 2016 at 04:49:21PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-centipede): New variable.
>
>> +    (synopsis "Predict transcription factor binding sites")
>
> And here I thought it would be a centipede genome ;)
>
>> +    (license (list license:gpl2+ license:gpl3+))))
>
> If something is gpl2+, can it also be gpl3+? I'm not sure, just asking
> for clarification.

Many R packages are released under any GPL version.  This allows the
package to be combined with packages that are released under the
unfortunate GPLv3 only and GPLv2 only license terms.

~~ Ricardo

Re: [PATCH] gnu: Add r-centipede.

[Ben Woodcroft]

On 03/05/16 00:49, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-centipede): New variable.
> ---
>   gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
>   1 file changed, 21 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 7d025ef..d7957cf 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -441,6 +441,27 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
>   Python.")
>       (license license:gpl2+)))
>   
> +(define-public r-centipede
> +  (package
> +    (name "r-centipede")
> +    (version "1.2")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append "http://download.r-forge.r-project.org/"
> +                                  "src/contrib/CENTIPEDE_" version ".tar.gz"))
> +              (sha256
> +               (base32
> +                "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
> +    (build-system r-build-system)
> +    (home-page "http://centipede.uchicago.edu/")
> +    (synopsis "Predict transcription factor binding sites")
> +    (description
> +     "Centipede fits a bayesian hierarchical mixture model to learn
> +transcription-factor-specific distribution of experimental data on a
> +particular cell-type for a set of candidate binding sites described by a
> +genetic motif.")
Perhaps this is just personal opinion but I prefer not to make the 
suggestion that experiments can only be done in the lab.

Also I don't think that sentence makes sense grammatically - 
s/distribution/distributions/ but even then, it doesn't learn the 
experimental data.
Maybe steal from the website, cut down a bit from this?
 >CENTIPEDE applies a hierarchical Bayesian mixture model to infer 
regions of the genome that are bound by particular transcription 
factors. It starts by identifying a set of candidate binding sites 
(e.g., sites that match a certain position weight matrix (PWM)), and 
then aims to classify the sites according to whether each site is bound 
or not bound by a TF. CENTIPEDE is an unsupervised learning algorithm 
that discriminates between two different types of motif instances using 
as much relevant information as possible.

Thanks,
ben

Re: [PATCH] gnu: Add r-centipede.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> On 03/05/16 00:49, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-centipede): New variable.
>> ---
>>   gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
>>   1 file changed, 21 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 7d025ef..d7957cf 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -441,6 +441,27 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
>>   Python.")
>>       (license license:gpl2+)))
>>
>> +(define-public r-centipede
>> +  (package
>> +    (name "r-centipede")
>> +    (version "1.2")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (string-append "http://download.r-forge.r-project.org/"
>> +                                  "src/contrib/CENTIPEDE_" version ".tar.gz"))
>> +              (sha256
>> +               (base32
>> +                "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
>> +    (build-system r-build-system)
>> +    (home-page "http://centipede.uchicago.edu/")
>> +    (synopsis "Predict transcription factor binding sites")
>> +    (description
>> +     "Centipede fits a bayesian hierarchical mixture model to learn
>> +transcription-factor-specific distribution of experimental data on a
>> +particular cell-type for a set of candidate binding sites described by a
>> +genetic motif.")
> Perhaps this is just personal opinion but I prefer not to make the
> suggestion that experiments can only be done in the lab.
>
> Also I don't think that sentence makes sense grammatically -
> s/distribution/distributions/ but even then, it doesn't learn the
> experimental data.
> Maybe steal from the website, cut down a bit from this?
>  >CENTIPEDE applies a hierarchical Bayesian mixture model to infer
> regions of the genome that are bound by particular transcription
> factors. It starts by identifying a set of candidate binding sites
> (e.g., sites that match a certain position weight matrix (PWM)), and
> then aims to classify the sites according to whether each site is bound
> or not bound by a TF. CENTIPEDE is an unsupervised learning algorithm
> that discriminates between two different types of motif instances using
> as much relevant information as possible.
>
> Thanks,
> ben

Not even a year later I pushed it to master as b91cfa22e with the
suggested change to the description.  I had totally forgotten about this
patch!

--
Ricardo

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