Patchwork gnu: Add multiqc.

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Submitter Ricardo Wurmus
Date June 28, 2016, 2:50 p.m.
Message ID <20160628145042.25341-1-ricardo.wurmus@mdc-berlin.de>
Download mbox | patch
Permalink /patch/13422/
State New
Headers show

Comments

Ricardo Wurmus - June 28, 2016, 2:50 p.m.
* gnu/packages/bioinformatics.scm (multiqc): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
Ricardo Wurmus - June 28, 2016, 2:56 p.m.
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)))
David Thompson - June 28, 2016, 3:30 p.m.
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
Ludovic Courtès - June 28, 2016, 10:02 p.m.
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’.
Ben Woodcroft - June 28, 2016, 11:05 p.m.
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
Ricardo Wurmus - July 5, 2016, 2:04 p.m.
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
Ricardo Wurmus - July 5, 2016, 2:07 p.m.
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

Patch

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)))