[bug#29017] [PATCH] gnu: Add gwl.

[bug#29017] [PATCH] gnu: Add gwl.

[Roel Janssen]

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Dear Guix,

I would like to add GWL.  For a lack of a better place, I chose the
bioinformatics module because that's where we use this package.

Thanks for your time!

Kind regards,
Roel Janssen


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From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 26 Oct 2017 22:46:50 +0200
Subject: [PATCH] gnu: Add gwl.

* gnu/packages/bioinformatics.scm (gwl): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 43a00f196..ac7320040 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -70,6 +70,7 @@
   #:use-module (gnu packages java)
   #:use-module (gnu packages ldc)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages lisp)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages man)
@@ -77,6 +78,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages ocaml)
+  #:use-module (gnu packages package-management)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages parallel)
   #:use-module (gnu packages pdf)
@@ -9755,6 +9757,37 @@ knowledge of gene annotation information.  GESS stands for the graph-based
 exon-skipping scanner detection scheme.")
     (license license:bsd-3)))
 
+(define-public gwl
+  (package
+    (name "gwl")
+    (version "0.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://git.roelj.com/attachments/"
+                                  "d804e310-b9c0-44b1-bd18-c7505e9f9d9b"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1x4swwp7kmhd57j3scii5c4h8swkcvab2r6mz7wxwwbx300wcqpy"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guix" ,guix)
+       ("guile" ,guile-2.2)
+       ("guile-commonmark" ,guile-commonmark)))
+    (home-page "https://www.guixwl.org")
+    (synopsis "Workflow management extension for GNU Guix")
+    (description "This project provides two subcommands to GNU Guix and
+introduces two record types that provide a workflow management extension built
+on top of GNU Guix.")
+    ;; The Scheme modules in guix/ and gnu/ are licensed GPL3+,
+    ;; the web interface modules in gwl/ are licensed AGPL3+,
+    ;; and the fonts included in this package are licensed OFL1.1.
+    (license (list license:gpl3+ license:agpl3+ license:silofl1.1))))
+
 (define-public phylip
   (package
     (name "phylip")
-- 
2.14.2

[bug#29017] [PATCH] gnu: Add gwl.

[Ludovic Courtès]

Hello!

Roel Janssen <roel@gnu.org> skribis:

> I would like to add GWL.  For a lack of a better place, I chose the
> bioinformatics module because that's where we use this package.

Awesome!  \o/

Perhaps that could go to package-management.scm?

> From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Thu, 26 Oct 2017 22:46:50 +0200
> Subject: [PATCH] gnu: Add gwl.
>
> * gnu/packages/bioinformatics.scm (gwl): New variable.

[...]

> +(define-public gwl
> +  (package
> +    (name "gwl")
> +    (version "0.1.0")
> +    (source (origin
> +              (method url-fetch)
> +              (uri (string-append "https://git.roelj.com/attachments/"
> +                                  "d804e310-b9c0-44b1-bd18-c7505e9f9d9b"))

Do you have a more “standard” URL, such as a cgit snapshot?  If not
that’s fine.

> +    (inputs
> +     `(("guix" ,guix)
> +       ("guile" ,guile-2.2)
> +       ("guile-commonmark" ,guile-commonmark)))

It might be that you either need to propagate Guix and CommonMark, or to
wrap the binaries that GWL provides (as is done in the ‘guix’ package),
no?

Otherwise LGTM, thank you!

Ludo’.

[bug#29017] [PATCH] gnu: Add gwl.

[Roel Janssen]

Ludovic Courtès writes:

> Hello!
>
> Roel Janssen <roel@gnu.org> skribis:
>
>> I would like to add GWL.  For a lack of a better place, I chose the
>> bioinformatics module because that's where we use this package.
>
> Awesome!  \o/
>
> Perhaps that could go to package-management.scm?

The new patch adds it to package-management.scm.

>
>> From eaa22755769973ba30600ae96bb92a5d6bad11dd Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Thu, 26 Oct 2017 22:46:50 +0200
>> Subject: [PATCH] gnu: Add gwl.
>>
>> * gnu/packages/bioinformatics.scm (gwl): New variable.
>
> [...]
>
>> +(define-public gwl
>> +  (package
>> +    (name "gwl")
>> +    (version "0.1.0")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (string-append "https://git.roelj.com/attachments/"
>> +                                  "d804e310-b9c0-44b1-bd18-c7505e9f9d9b"))
>
> Do you have a more “standard” URL, such as a cgit snapshot?  If not
> that’s fine.

This I found a bit weird about Gogs.  Custom-uploaded tarballs get these
weird URLs.  I uploaded the same tarball to guixwl.org, and adjusted the
recipe to use that URL.

>
>> +    (inputs
>> +     `(("guix" ,guix)
>> +       ("guile" ,guile-2.2)
>> +       ("guile-commonmark" ,guile-commonmark)))
>
> It might be that you either need to propagate Guix and CommonMark, or to
> wrap the binaries that GWL provides (as is done in the ‘guix’ package),
> no?

I added guix and guile-commonmark to the propagated-inputs.

>
> Otherwise LGTM, thank you!
>
> Ludo’.

Thanks for your quick response!  I pushed the new patch in 58a308e0b.

Kind regards,
Roel Janssen

bug#29017: [PATCH] gnu: Add gwl.

[Roel Janssen]