* [PATCH] gnu: Add bio-blastxmlparser.
@ 2015-09-16 6:53 Pjotr Prins
2015-09-17 6:46 ` Pjotr Prins
0 siblings, 1 reply; 3+ messages in thread
From: Pjotr Prins @ 2015-09-16 6:53 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f34211..b9e1158 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2642,3 +2642,28 @@ position for indels. Bio-locus allows users to store this chr+pos or
chr+pos+alt information in a database.")
(home-page "https://github.com/pjotrp/bio-locus")
(license license:expat)))
+
+(define-public bio-blastxmlparser
+ (package
+ (name "bio-blastxmlparser")
+ (version "2.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-blastxmlparser" version))
+ (sha256
+ (base32
+ "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
+ (build-system ruby-build-system)
+ (propagated-inputs
+ `(("ruby-bio-logger" ,ruby-bio-logger)
+ ("ruby-nokogiri" ,ruby-nokogiri)))
+ (inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Fast big data BLAST XML parser and library")
+ (description "Very fast parallel big-data BLAST XML file parser
+which can be used as command line utility. Use blastxmlparser to:
+Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF,
+JSON-LD, HTML, csv, tabular output etc.")
+ (home-page "http://github.com/pjotrp/blastxmlparser")
+ (license license:expat)))
--
2.4.3
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add bio-blastxmlparser.
2015-09-16 6:53 [PATCH] gnu: Add bio-blastxmlparser Pjotr Prins
@ 2015-09-17 6:46 ` Pjotr Prins
2015-09-28 10:26 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Pjotr Prins @ 2015-09-17 6:46 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
This one is in the queue.
On Wed, Sep 16, 2015 at 08:53:13AM +0200, Pjotr Prins wrote:
> * gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
> ---
> gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
> 1 file changed, 25 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 1f34211..b9e1158 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -2642,3 +2642,28 @@ position for indels. Bio-locus allows users to store this chr+pos or
> chr+pos+alt information in a database.")
> (home-page "https://github.com/pjotrp/bio-locus")
> (license license:expat)))
> +
> +(define-public bio-blastxmlparser
> + (package
> + (name "bio-blastxmlparser")
> + (version "2.0.4")
> + (source
> + (origin
> + (method url-fetch)
> + (uri (rubygems-uri "bio-blastxmlparser" version))
> + (sha256
> + (base32
> + "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
> + (build-system ruby-build-system)
> + (propagated-inputs
> + `(("ruby-bio-logger" ,ruby-bio-logger)
> + ("ruby-nokogiri" ,ruby-nokogiri)))
> + (inputs
> + `(("ruby-rspec" ,ruby-rspec)))
> + (synopsis "Fast big data BLAST XML parser and library")
> + (description "Very fast parallel big-data BLAST XML file parser
> +which can be used as command line utility. Use blastxmlparser to:
> +Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF,
> +JSON-LD, HTML, csv, tabular output etc.")
> + (home-page "http://github.com/pjotrp/blastxmlparser")
> + (license license:expat)))
> --
> 2.4.3
>
>
--
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: Add bio-blastxmlparser.
2015-09-17 6:46 ` Pjotr Prins
@ 2015-09-28 10:26 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-09-28 10:26 UTC (permalink / raw)
To: Pjotr Prins; +Cc: guix-devel
Hi Pjotr,
> This one is in the queue.
>
> On Wed, Sep 16, 2015 at 08:53:13AM +0200, Pjotr Prins wrote:
>> * gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
I pushed this with minor modifications (minor adjustments to the
description, little formatting tweaks, C-M-q on the expression).
I couldn’t apply the patch directly from the email for some reason (“git
am” on the email file failed inexplicably), so I had to recommit this
and manually set the author to you.
Thanks for the contribution!
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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2015-09-16 6:53 [PATCH] gnu: Add bio-blastxmlparser Pjotr Prins
2015-09-17 6:46 ` Pjotr Prins
2015-09-28 10:26 ` Ricardo Wurmus
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