[PATCH] gnu: Add multiqc.

[PATCH] gnu: Add multiqc.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (multiqc): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 04ed769..45595d0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5321,3 +5321,33 @@ group or two ChIP groups run under different conditions.")
       (description "This program compares version strings.  It intends to be a
 replacement for strverscmp.")
       (license license:gpl3+))))
+
+(define-public multiqc
+  (package
+    (name "multiqc")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/23/d9/95a5e62eea95f220007d7a6683d0da1ee1d9f99e6932bcff793b6601ef15/multiqc-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-jinja2" ,python-jinja2)
+       ("python-simplejson" ,python-simplejson)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-click" ,python-click)
+       ("python-matplotlib" ,python-matplotlib)))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "http://multiqc.info")
+    (synopsis "Aggregate bioinformatics analysis reports")
+    (description
+     "MultiQC is a tool to aggregate bioinformatics results across many
+samples into a single report.  It contains modules for a large number of
+common bioinformatics tools.")
+    (license license:gpl3)))
-- 
2.8.4

Re: [PATCH] gnu: Add multiqc.

[Ricardo Wurmus]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> * gnu/packages/bioinformatics.scm (multiqc): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
>  1 file changed, 30 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 04ed769..45595d0 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5321,3 +5321,33 @@ group or two ChIP groups run under different conditions.")
>        (description "This program compares version strings.  It intends to be a
>  replacement for strverscmp.")
>        (license license:gpl3+))))
> +
> +(define-public multiqc
> +  (package
> +    (name "multiqc")
> +    (version "0.6")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://pypi.python.org/packages/23/d9/95a5e62eea95f220007d7a6683d0da1ee1d9f99e6932bcff793b6601ef15/multiqc-"
> +             version ".tar.gz"))
> +       (sha256
> +        (base32
> +         "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
> +    (build-system python-build-system)
> +    (propagated-inputs
> +     `(("python-jinja2" ,python-jinja2)
> +       ("python-simplejson" ,python-simplejson)
> +       ("python-pyyaml" ,python-pyyaml)
> +       ("python-click" ,python-click)
> +       ("python-matplotlib" ,python-matplotlib)))

I sent this patch too early.  The final version also has “python-numpy”
among its propagated inputs.  Other than that there are no changes.

> +    (native-inputs
> +     `(("python-setuptools" ,python-setuptools)))
> +    (home-page "http://multiqc.info")
> +    (synopsis "Aggregate bioinformatics analysis reports")
> +    (description
> +     "MultiQC is a tool to aggregate bioinformatics results across many
> +samples into a single report.  It contains modules for a large number of
> +common bioinformatics tools.")
> +    (license license:gpl3)))

Re: [PATCH] gnu: Add multiqc.

[Thompson, David]

On Tue, Jun 28, 2016 at 10:50 AM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
> * gnu/packages/bioinformatics.scm (multiqc): New variable.

LGTM!

- Dave

Re: [PATCH] gnu: Add multiqc.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> * gnu/packages/bioinformatics.scm (multiqc): New variable.

[...]

> +    (license license:gpl3)))

Make sure it’s v3-only, but otherwise LGTM too!

Ludo’.

Re: [PATCH] gnu: Add multiqc.

[Ben Woodcroft]

On 29/06/16 00:56, Ricardo Wurmus wrote:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> * gnu/packages/bioinformatics.scm (multiqc): New variable.
>> ---
>>   gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
>>   1 file changed, 30 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 04ed769..45595d0 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -5321,3 +5321,33 @@ group or two ChIP groups run under different conditions.")
>>         (description "This program compares version strings.  It intends to be a
>>   replacement for strverscmp.")
>>         (license license:gpl3+))))
>> +
>> +(define-public multiqc
>> +  (package
>> +    (name "multiqc")
>> +    (version "0.6")
>> +    (source
>> +     (origin
>> +       (method url-fetch)
>> +       (uri (string-append
>> +             "https://pypi.python.org/packages/23/d9/95a5e62eea95f220007d7a6683d0da1ee1d9f99e6932bcff793b6601ef15/multiqc-"
>> +             version ".tar.gz"))

I think 'pypi-uri' would be better here, now that it handles these kinds 
of URLs. We should change 'import' so that these long URLs are not printed.

Thanks for the patch.
ben

Re: [PATCH] gnu: Add multiqc.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> On 29/06/16 00:56, Ricardo Wurmus wrote:
>> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>>
>>> * gnu/packages/bioinformatics.scm (multiqc): New variable.
>>> ---
>>>   gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
>>>   1 file changed, 30 insertions(+)
>>>
>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>> index 04ed769..45595d0 100644
>>> --- a/gnu/packages/bioinformatics.scm
>>> +++ b/gnu/packages/bioinformatics.scm
>>> @@ -5321,3 +5321,33 @@ group or two ChIP groups run under different conditions.")
>>>         (description "This program compares version strings.  It intends to be a
>>>   replacement for strverscmp.")
>>>         (license license:gpl3+))))
>>> +
>>> +(define-public multiqc
>>> +  (package
>>> +    (name "multiqc")
>>> +    (version "0.6")
>>> +    (source
>>> +     (origin
>>> +       (method url-fetch)
>>> +       (uri (string-append
>>> +             "https://pypi.python.org/packages/23/d9/95a5e62eea95f220007d7a6683d0da1ee1d9f99e6932bcff793b6601ef15/multiqc-"
>>> +             version ".tar.gz"))
>
> I think 'pypi-uri' would be better here, now that it handles these kinds 
> of URLs. We should change 'import' so that these long URLs are not printed.

Oh, I missed that update to “pypi-uri”.  I’ll push with this change.
Thanks!

~~ Ricardo

Re: [PATCH] gnu: Add multiqc.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> * gnu/packages/bioinformatics.scm (multiqc): New variable.
>
> [...]
>
>> +    (license license:gpl3)))
>
> Make sure it’s v3-only, but otherwise LGTM too!

The only mention of a license is in “setup.py” declaring it to be
“GPLv3”.  As there is no indication that what is actually meant is
really “GPLv3+” I think I have no choice but to use “gpl3” here.

~~ Ricardo