* [PATCH] gnu: Add r-genomationdata.
@ 2016-05-23 14:57 Ricardo Wurmus
2016-05-23 18:09 ` Efraim Flashner
0 siblings, 1 reply; 6+ messages in thread
From: Ricardo Wurmus @ 2016-05-23 14:57 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbaae12..51c371c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5002,6 +5002,32 @@ genomic feature data as long as it has minimal information on the locations of
genomic intervals. In addition, it can use BAM or BigWig files as input.")
(license license:artistic2.0)))
+(define-public r-genomationdata
+ (package
+ (name "r-genomationdata")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://bioconductor.org/packages/"
+ "release/data/experiment/src/contrib/"
+ "genomationData_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1xzq2j722d8lcn5bc3aq3yb34xwis2d0bpsf6jsq4xw1bg0bsy79"))))
+ (build-system r-build-system)
+ (arguments `(#:substitutable? #f))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Experimental data for use with the genomation package")
+ (description
+ "This package contains experimental genetic data for use with the
+genomation package. Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+ (license license:gpl3+)))
+
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
--
2.7.3
^ permalink raw reply related [flat|nested] 6+ messages in thread* Re: [PATCH] gnu: Add r-genomationdata.
2016-05-23 14:57 [PATCH] gnu: Add r-genomationdata Ricardo Wurmus
@ 2016-05-23 18:09 ` Efraim Flashner
2016-05-24 6:36 ` Ricardo Wurmus
0 siblings, 1 reply; 6+ messages in thread
From: Efraim Flashner @ 2016-05-23 18:09 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 2271 bytes --]
On Mon, May 23, 2016 at 04:57:16PM +0200, Ricardo Wurmus wrote:
> * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
> ---
> gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
> 1 file changed, 26 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index fbaae12..51c371c 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5002,6 +5002,32 @@ genomic feature data as long as it has minimal information on the locations of
> genomic intervals. In addition, it can use BAM or BigWig files as input.")
> (license license:artistic2.0)))
>
> +(define-public r-genomationdata
> + (package
> + (name "r-genomationdata")
> + (version "1.4.0")
> + (source (origin
> + (method url-fetch)
> + ;; We cannot use bioconductor-uri here because this tarball is
> + ;; located under "data/annotation/" instead of "bioc/".
> + (uri (string-append "https://bioconductor.org/packages/"
> + "release/data/experiment/src/contrib/"
> + "genomationData_" version ".tar.gz"))
> + (sha256
> + (base32
> + "1xzq2j722d8lcn5bc3aq3yb34xwis2d0bpsf6jsq4xw1bg0bsy79"))))
> + (build-system r-build-system)
> + (arguments `(#:substitutable? #f))
^^^^
why not?
> + (native-inputs
> + `(("r-knitr" ,r-knitr)))
> + (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
> + (synopsis "Experimental data for use with the genomation package")
> + (description
> + "This package contains experimental genetic data for use with the
> +genomation package. Included are Chip Seq, Methylation and Cage data,
> +downloaded from Encode.")
> + (license license:gpl3+)))
> +
> (define-public r-org-hs-eg-db
> (package
> (name "r-org-hs-eg-db")
> --
> 2.7.3
>
Looks good
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 819 bytes --]
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: [PATCH] gnu: Add r-genomationdata.
2016-05-23 18:09 ` Efraim Flashner
@ 2016-05-24 6:36 ` Ricardo Wurmus
2016-05-24 7:09 ` Efraim Flashner
2016-05-24 9:52 ` Ludovic Courtès
0 siblings, 2 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2016-05-24 6:36 UTC (permalink / raw)
To: Efraim Flashner; +Cc: guix-devel
Efraim Flashner <efraim@flashner.co.il> writes:
> On Mon, May 23, 2016 at 04:57:16PM +0200, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
>> ---
[...]
>> + (arguments `(#:substitutable? #f))
> ^^^^
> why not?
Because it’s an R data package, i.e. it’s a large download taking up
space on hydra; it’s the same for all architechtures and there’s no real
advantage in providing a binary substitute.
We’ve done the same for the genome data packages. It was more clear cut
then, because the download was about ten times bigger.
Still, I didn’t want to waste space on hydra with a substitute for
something that’s mostly a simple download.
~~ Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] gnu: Add r-genomationdata.
2016-05-24 6:36 ` Ricardo Wurmus
@ 2016-05-24 7:09 ` Efraim Flashner
2016-05-24 9:52 ` Ludovic Courtès
1 sibling, 0 replies; 6+ messages in thread
From: Efraim Flashner @ 2016-05-24 7:09 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 1244 bytes --]
On Tue, May 24, 2016 at 08:36:22AM +0200, Ricardo Wurmus wrote:
>
> Efraim Flashner <efraim@flashner.co.il> writes:
>
> > On Mon, May 23, 2016 at 04:57:16PM +0200, Ricardo Wurmus wrote:
> >> * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
> >> ---
>
> [...]
>
> >> + (arguments `(#:substitutable? #f))
> > ^^^^
> > why not?
>
> Because it’s an R data package, i.e. it’s a large download taking up
> space on hydra; it’s the same for all architechtures and there’s no real
> advantage in providing a binary substitute.
>
> We’ve done the same for the genome data packages. It was more clear cut
> then, because the download was about ten times bigger.
>
> Still, I didn’t want to waste space on hydra with a substitute for
> something that’s mostly a simple download.
>
> ~~ Ricardo
I was a little short with words, what I meant to write was "we add a
comment when we have #:tests? #f, should we add a comment here too?"
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 819 bytes --]
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] gnu: Add r-genomationdata.
2016-05-24 6:36 ` Ricardo Wurmus
2016-05-24 7:09 ` Efraim Flashner
@ 2016-05-24 9:52 ` Ludovic Courtès
2016-05-31 14:30 ` Ricardo Wurmus
1 sibling, 1 reply; 6+ messages in thread
From: Ludovic Courtès @ 2016-05-24 9:52 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Efraim Flashner <efraim@flashner.co.il> writes:
>
>> On Mon, May 23, 2016 at 04:57:16PM +0200, Ricardo Wurmus wrote:
>>> * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
>>> ---
>
> [...]
>
>>> + (arguments `(#:substitutable? #f))
>> ^^^^
>> why not?
>
> Because it’s an R data package, i.e. it’s a large download taking up
> space on hydra; it’s the same for all architechtures and there’s no real
> advantage in providing a binary substitute.
Makes sense. Maybe just mention it in a comment above.
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 6+ messages in thread
* Re: [PATCH] gnu: Add r-genomationdata.
2016-05-24 9:52 ` Ludovic Courtès
@ 2016-05-31 14:30 ` Ricardo Wurmus
0 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2016-05-31 14:30 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> Efraim Flashner <efraim@flashner.co.il> writes:
>>
>>> On Mon, May 23, 2016 at 04:57:16PM +0200, Ricardo Wurmus wrote:
>>>> * gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
>>>> ---
>>
>> [...]
>>
>>>> + (arguments `(#:substitutable? #f))
>>> ^^^^
>>> why not?
>>
>> Because it’s an R data package, i.e. it’s a large download taking up
>> space on hydra; it’s the same for all architechtures and there’s no real
>> advantage in providing a binary substitute.
>
> Makes sense. Maybe just mention it in a comment above.
I added a comment and pushed. Thanks!
~~ Ricardo
^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2016-05-31 14:31 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-05-23 14:57 [PATCH] gnu: Add r-genomationdata Ricardo Wurmus
2016-05-23 18:09 ` Efraim Flashner
2016-05-24 6:36 ` Ricardo Wurmus
2016-05-24 7:09 ` Efraim Flashner
2016-05-24 9:52 ` Ludovic Courtès
2016-05-31 14:30 ` Ricardo Wurmus
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).