* [PATCH] gnu: Add multiqc.
@ 2016-06-28 14:50 Ricardo Wurmus
2016-06-28 14:56 ` Ricardo Wurmus
` (2 more replies)
0 siblings, 3 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-06-28 14:50 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 7+ messages in thread* Re: [PATCH] gnu: Add multiqc.
2016-06-28 14:50 [PATCH] gnu: Add multiqc Ricardo Wurmus
@ 2016-06-28 14:56 ` Ricardo Wurmus
2016-06-28 23:05 ` Ben Woodcroft
2016-06-28 15:30 ` Thompson, David
2016-06-28 22:02 ` Ludovic Courtès
2 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2016-06-28 14:56 UTC (permalink / raw)
To: guix-devel
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)))
^ permalink raw reply [flat|nested] 7+ messages in thread* Re: [PATCH] gnu: Add multiqc.
2016-06-28 14:56 ` Ricardo Wurmus
@ 2016-06-28 23:05 ` Ben Woodcroft
2016-07-05 14:04 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Ben Woodcroft @ 2016-06-28 23:05 UTC (permalink / raw)
To: Ricardo Wurmus, guix-devel
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] gnu: Add multiqc.
2016-06-28 23:05 ` Ben Woodcroft
@ 2016-07-05 14:04 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-07-05 14:04 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] gnu: Add multiqc.
2016-06-28 14:50 [PATCH] gnu: Add multiqc Ricardo Wurmus
2016-06-28 14:56 ` Ricardo Wurmus
@ 2016-06-28 15:30 ` Thompson, David
2016-06-28 22:02 ` Ludovic Courtès
2 siblings, 0 replies; 7+ messages in thread
From: Thompson, David @ 2016-06-28 15:30 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] gnu: Add multiqc.
2016-06-28 14:50 [PATCH] gnu: Add multiqc Ricardo Wurmus
2016-06-28 14:56 ` Ricardo Wurmus
2016-06-28 15:30 ` Thompson, David
@ 2016-06-28 22:02 ` Ludovic Courtès
2016-07-05 14:07 ` Ricardo Wurmus
2 siblings, 1 reply; 7+ messages in thread
From: Ludovic Courtès @ 2016-06-28 22:02 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
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’.
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] gnu: Add multiqc.
2016-06-28 22:02 ` Ludovic Courtès
@ 2016-07-05 14:07 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-07-05 14:07 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2016-07-05 14:07 UTC | newest]
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2016-06-28 14:50 [PATCH] gnu: Add multiqc Ricardo Wurmus
2016-06-28 14:56 ` Ricardo Wurmus
2016-06-28 23:05 ` Ben Woodcroft
2016-07-05 14:04 ` Ricardo Wurmus
2016-06-28 15:30 ` Thompson, David
2016-06-28 22:02 ` Ludovic Courtès
2016-07-05 14:07 ` Ricardo Wurmus
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