* [PATCH] gnu: Add ruby-bio-locus.
@ 2015-09-14 13:24 Pjotr Prins
2015-09-14 14:01 ` Thompson, David
0 siblings, 1 reply; 6+ messages in thread
From: Pjotr Prins @ 2015-09-14 13:24 UTC (permalink / raw)
To: David Thompson; +Cc: guix-devel
* gnu/packages/ruby.scm (ruby-bio-locus): New variable.
---
gnu/packages/ruby.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index ee0acc8..0a0fc1a 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1124,3 +1124,23 @@ it unifies the API for web servers, web frameworks, and software in between
into a single method call.")
(home-page "http://rack.github.io/")
(license license:expat)))
+
+(define-public ruby-bio-locus
+ (package
+ (name "ruby-bio-locus")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-locus" version))
+ (sha256
+ (base32
+ "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
+ (build-system ruby-build-system)
+ (native-inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Tool for fast querying of genome locations")
+ (description "This tabix-like tool essentially allows your to
+store this chr+pos or chr+pos+alt information in a fast database.")
+ (home-page "https://github.com/pjotrp/bio-locus")
+ (license license:expat)))
--
2.4.3
^ permalink raw reply related [flat|nested] 6+ messages in thread* Re: [PATCH] gnu: Add ruby-bio-locus.
2015-09-14 13:24 [PATCH] gnu: Add ruby-bio-locus Pjotr Prins
@ 2015-09-14 14:01 ` Thompson, David
2015-09-14 14:18 ` Pjotr Prins
0 siblings, 1 reply; 6+ messages in thread
From: Thompson, David @ 2015-09-14 14:01 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
On Mon, Sep 14, 2015 at 9:24 AM, Pjotr Prins <pjotr.public12@thebird.nl> wrote:
> * gnu/packages/ruby.scm (ruby-bio-locus): New variable.
Awesome! Just a couple of minor comments below.
> ---
> gnu/packages/ruby.scm | 20 ++++++++++++++++++++
> 1 file changed, 20 insertions(+)
>
> diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
> index ee0acc8..0a0fc1a 100644
> --- a/gnu/packages/ruby.scm
> +++ b/gnu/packages/ruby.scm
> @@ -1124,3 +1124,23 @@ it unifies the API for web servers, web frameworks, and software in between
> into a single method call.")
> (home-page "http://rack.github.io/")
> (license license:expat)))
> +
> +(define-public ruby-bio-locus
> + (package
> + (name "ruby-bio-locus")
This is an application, not a library, correct? If so, I think it
would be best to name it just "bio-locus" and put it in the (gnu
packages bioinformatics) module. WDYT?
> + (version "0.0.7")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (rubygems-uri "bio-locus" version))
> + (sha256
> + (base32
> + "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
> + (build-system ruby-build-system)
> + (native-inputs
> + `(("ruby-rspec" ,ruby-rspec)))
> + (synopsis "Tool for fast querying of genome locations")
> + (description "This tabix-like tool essentially allows your to
> +store this chr+pos or chr+pos+alt information in a fast database.")
How about something more descriptive? Here's a modified snippet from
your README:
Bio-locus is a tool for fast querying of genome locations.
Many file formats in bioinformatics contain records that start with a
chromosome name and a position for a SNP, or a start-end position
for indels.
Bio-locus allows users to store this chr+pos or chr+pos+alt information in a
fast database.
> + (home-page "https://github.com/pjotrp/bio-locus")
> + (license license:expat)))
> --
> 2.4.3
>
Thanks! Keep 'em coming!
- Dave
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: [PATCH] gnu: Add ruby-bio-locus.
2015-09-14 14:01 ` Thompson, David
@ 2015-09-14 14:18 ` Pjotr Prins
2015-09-14 14:30 ` Thompson, David
0 siblings, 1 reply; 6+ messages in thread
From: Pjotr Prins @ 2015-09-14 14:18 UTC (permalink / raw)
To: Thompson, David; +Cc: guix-devel
I am at the biohackathon in Japan - planning to submit more of these.
Many people here are interested in our work :)
http://2015.biohackathon.org/hackathon
OK, yes, it probably belongs in bioinformatics.scm. Note the gem
contains tests that pass ;). I love the abstraction that guix offers
for gems. I added to
https://github.com/pjotrp/guix-notes/blob/master/RUBY.org#adding-a-ruby-gem-to-guix
Pj.
On Mon, Sep 14, 2015 at 10:01:40AM -0400, Thompson, David wrote:
> On Mon, Sep 14, 2015 at 9:24 AM, Pjotr Prins <pjotr.public12@thebird.nl> wrote:
> > * gnu/packages/ruby.scm (ruby-bio-locus): New variable.
>
> Awesome! Just a couple of minor comments below.
>
> > ---
> > gnu/packages/ruby.scm | 20 ++++++++++++++++++++
> > 1 file changed, 20 insertions(+)
> >
> > diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
> > index ee0acc8..0a0fc1a 100644
> > --- a/gnu/packages/ruby.scm
> > +++ b/gnu/packages/ruby.scm
> > @@ -1124,3 +1124,23 @@ it unifies the API for web servers, web frameworks, and software in between
> > into a single method call.")
> > (home-page "http://rack.github.io/")
> > (license license:expat)))
> > +
> > +(define-public ruby-bio-locus
> > + (package
> > + (name "ruby-bio-locus")
>
> This is an application, not a library, correct? If so, I think it
> would be best to name it just "bio-locus" and put it in the (gnu
> packages bioinformatics) module. WDYT?
>
> > + (version "0.0.7")
> > + (source
> > + (origin
> > + (method url-fetch)
> > + (uri (rubygems-uri "bio-locus" version))
> > + (sha256
> > + (base32
> > + "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
> > + (build-system ruby-build-system)
> > + (native-inputs
> > + `(("ruby-rspec" ,ruby-rspec)))
> > + (synopsis "Tool for fast querying of genome locations")
> > + (description "This tabix-like tool essentially allows your to
> > +store this chr+pos or chr+pos+alt information in a fast database.")
>
> How about something more descriptive? Here's a modified snippet from
> your README:
>
> Bio-locus is a tool for fast querying of genome locations.
> Many file formats in bioinformatics contain records that start with a
> chromosome name and a position for a SNP, or a start-end position
> for indels.
> Bio-locus allows users to store this chr+pos or chr+pos+alt information in a
> fast database.
>
> > + (home-page "https://github.com/pjotrp/bio-locus")
> > + (license license:expat)))
> > --
> > 2.4.3
> >
>
> Thanks! Keep 'em coming!
>
> - Dave
>
--
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: [PATCH] gnu: Add ruby-bio-locus.
2015-09-14 14:18 ` Pjotr Prins
@ 2015-09-14 14:30 ` Thompson, David
2015-09-14 14:32 ` Pjotr Prins
0 siblings, 1 reply; 6+ messages in thread
From: Thompson, David @ 2015-09-14 14:30 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
On Mon, Sep 14, 2015 at 10:18 AM, Pjotr Prins <pjotr.public12@thebird.nl> wrote:
> I am at the biohackathon in Japan - planning to submit more of these.
> Many people here are interested in our work :)
>
> http://2015.biohackathon.org/hackathon
Awesome. Thanks for giving Guix such good promotion!
> OK, yes, it probably belongs in bioinformatics.scm. Note the gem
> contains tests that pass ;). I love the abstraction that guix offers
> for gems.
Yes, I was happy to see 'ruby-rspec' in the native inputs.
> I added to
>
> https://github.com/pjotrp/guix-notes/blob/master/RUBY.org#adding-a-ruby-gem-to-guix
Great! I think you should mention 'guix import gem' because it
calculates the gem archive's hash for you and generates a basic
package expression, giving newcomers a better starting point to tweak
from.
Can you send an updated patch for bio-locus? Thanks!
- Dave
^ permalink raw reply [flat|nested] 6+ messages in thread
* [PATCH] gnu: Add ruby-bio-locus.
2015-09-14 14:30 ` Thompson, David
@ 2015-09-14 14:32 ` Pjotr Prins
2015-09-14 19:19 ` Thompson, David
0 siblings, 1 reply; 6+ messages in thread
From: Pjotr Prins @ 2015-09-14 14:32 UTC (permalink / raw)
To: Thompson, David; +Cc: guix-devel
* gnu/packages/ruby.scm (ruby-bio-locus): New variable.
---
gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03eb2df..c4ba0e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2616,3 +2616,27 @@ data in the form of VCF files.")
;; The license is declared as LGPLv3 in the README and
;; at http://vcftools.sourceforge.net/license.html
(license license:lgpl3)))
+
+(define-public bio-locus
+ (package
+ (name "bio-locus")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-locus" version))
+ (sha256
+ (base32
+ "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
+ (build-system ruby-build-system)
+ (native-inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Tool for fast querying of genome locations")
+ (description
+ "Bio-locus is a tabix-like tool for fast querying of genome
+locations. Many file formats in bioinformatics contain records that
+start with a chromosome name and a position for a SNP, or a start-end
+position for indels. Bio-locus allows users to store this chr+pos or
+chr+pos+alt information in a fast database.")
+ (home-page "https://github.com/pjotrp/bio-locus")
+ (license license:expat)))
--
2.4.3
^ permalink raw reply related [flat|nested] 6+ messages in thread
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2015-09-14 13:24 [PATCH] gnu: Add ruby-bio-locus Pjotr Prins
2015-09-14 14:01 ` Thompson, David
2015-09-14 14:18 ` Pjotr Prins
2015-09-14 14:30 ` Thompson, David
2015-09-14 14:32 ` Pjotr Prins
2015-09-14 19:19 ` Thompson, David
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