I modified the PYTHONPATH in htseq_count
(http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) and cutadapt
(http://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt). It would be
great to have some common dependencies setup in the toolshed such as
numpy, etc.
Lance
Björn Grüning wrote:
Hi
On Wed, Apr 17, 2013 at 9:24 PM, Björn Grüning wrote:
> Hi Peter,
>
>> On Wed, Apr 17, 2013 at 6:05 PM, James Taylor wrote:
>> > No it does not have root, and it is very important that we not install
>> > anything at the system level since we need to maintain version
>> > isolation. We should alwa
Hi Peter,
> On Wed, Apr 17, 2013 at 6:05 PM, James Taylor wrote:
> > No it does not have root, and it is very important that we not install
> > anything at the system level since we need to maintain version
> > isolation. We should always be able to inject things into the
> > environment so that
On Wed, Apr 17, 2013 at 2:43 PM, Peter Cock wrote:
> Does
> that mean installing Python modules locally and then
> manipulating the PYTHONPATH is the best plan?
That's what I had in mind, there may be better ways though.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Apr 17, 2013 at 6:05 PM, James Taylor wrote:
> No it does not have root, and it is very important that we not install
> anything at the system level since we need to maintain version
> isolation. We should always be able to inject things into the
> environment so that Python/Perl/R look in
No it does not have root, and it is very important that we not install
anything at the system level since we need to maintain version
isolation. We should always be able to inject things into the
environment so that Python/Perl/R look in the right place.
--
James Taylor, Assistant Professor, Biolo
Hi all,
Galaxy has long had two very simple (but largely unused)
dependency mechanisms in a tool's XML (pre-dating the
tool shed), for binaries and Python modules, e.g.
numpy
taxBuilder
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirement.3E_tag_set
This has si
On Tue, Apr 16, 2013 at 5:23 PM, Peter Cock wrote:
> Hi all,
>
> Galaxy has long had two very simple (but largely unused)
> dependency mechanisms in a tool's XML (pre-dating the
> tool shed), for binaries and Python modules, e.g.
>
>
> numpy
> taxBuilder
>
>
> http://wiki.galaxyproject
