[PATCH] gnu: Add bio-blastxmlparser.

[PATCH] gnu: Add bio-blastxmlparser.

[Pjotr Prins]

* 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

Re: [PATCH] gnu: Add bio-blastxmlparser.

[Pjotr Prins]

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
> 
> 

-- 

Re: [PATCH] gnu: Add bio-blastxmlparser.

[Ricardo Wurmus]

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