2:20 p.m.
Hi,
I followed the advice for multiple installed python versions to set
~galaxy/galaxy-python/python and set the environment for the galaxy user
to have that in the PATH
Problem is, when a job is started on GridEngine, it does not use the
"-V" flag to inherit the environment. So it runs with a different python
version and more important it does not set LD_LIBRARY_PATH and fails for
some tools which need some special lib. (libRblas in this case)
Where can I fix that?
regards, Andreas
2:33 p.m.
Andreas Kuntzagk wrote:
I followed the advice for multiple installed python versions to set
~galaxy/galaxy-python/python and set the environment for the galaxy user
to have that in the PATH
Problem is, when a job is started on GridEngine, it does not use the
"-V" flag to inherit the environment. So it runs with a different python
version and more important it does not set LD_LIBRARY_PATH and fails for
some tools which need some special lib. (libRblas in this case)
Where can I fix that?
Andreas,
You should be able to set it in your shell's startup files (like
~/.bash_profile).
--nate
3:06 p.m.
Hi,
> I followed the advice for multiple installed python versions to
set
> ~galaxy/galaxy-python/python and set the environment for the galaxy
> user to have that in the PATH
>
> Problem is, when a job is started on GridEngine, it does not use the
> "-V" flag to inherit the environment. So it runs with a different
> python version and more important it does not set LD_LIBRARY_PATH and
> fails for some tools which need some special lib. (libRblas in this
> case)
> Where can I fix that?
Andreas,
You should be able to set it in your shell's startup files (like
~/.bash_profile).
It is set in ~/.bashrc, which is source by ~/.bash_profile. If I
normally login to a cluster node via ssh it is set correctly. But if I
qsub a job, it is not read. Except when I set the "-V" switch. So I
either need to change gridengines behaviour or make galaxy use that switch.
Is there a easy way to config how to submit cluster jobs?
Regards, Andreas
3:51 p.m.
Andreas Kuntzagk wrote:
It is set in ~/.bashrc, which is source by ~/.bash_profile. If I
normally login to a cluster node via ssh it is set correctly. But if I
qsub a job, it is not read. Except when I set the "-V" switch. So I
either need to change gridengines behaviour or make galaxy use that switch.
Is there a easy way to config how to submit cluster jobs?
Andreas,
SGE must not be running the shell as a login or interactive shell, which
PBS does. You may want to check the 'INVOCATION' section of the bash(1)
man page to see how you can force this.
If you can't change how your shell is run by SGE, you could add what you
need to the SGE job template in:
galaxy_dist/lib/galaxy/jobs/runners/sge.py
but this would be an ugly hack.
--nate
4:18 p.m.
SGE supports per-user defaults file called "~/.sge_request" ,
which can be used to set job's environment variables (and other qsub parameters).
I think it was mentioned in the galaxy-dev list (I don't remember by whom).
Example:
============
$ cat ~/.sge_request
-v PERL5LIB=/data/hannon/gordon/perl_modules/lib64/perl5
-v DUMMY=HELLO
============
Will add two environment variables (PERL5LIB and DUMMY) to each qsub job.
I guess this way you can also change the PATH.
see "man sge_request" or "man ge_request" (in some places it is
mentioned as "ge_request" instead of "sge_request").
"man qsub" tells which options take precedence ( command-line VS script VS
user-sge_request VS gloval-sge_request ).
Tested with SGE 6.1 and 6.2u3.
-gordon
Nate Coraor wrote, On 10/20/2009 11:51 AM:
Andreas Kuntzagk wrote:
> It is set in ~/.bashrc, which is source by ~/.bash_profile. If I
> normally login to a cluster node via ssh it is set correctly. But if I
> qsub a job, it is not read. Except when I set the "-V" switch. So I
> either need to change gridengines behaviour or make galaxy use that switch.
>
> Is there a easy way to config how to submit cluster jobs?
Andreas,
SGE must not be running the shell as a login or interactive shell, which
PBS does. You may want to check the 'INVOCATION' section of the bash(1)
man page to see how you can force this.
If you can't change how your shell is run by SGE, you could add what you
need to the SGE job template in:
galaxy_dist/lib/galaxy/jobs/runners/sge.py
but this would be an ugly hack.
--nate
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9:22 a.m.
New subject: SVG images in tool.xml don't load
Hi,
I have some tools that produce SVG images. These load just fine in a browser when they are
in the middle part of a galaxy browser window as tool output. But now I've added some
example images as documentation in the help section of the *.xml tool config files using
the reStructuredText syntax like this:
.. image:: /images/custom_galaxy_tools/ExtractModificationSiteSequenceContext.svg
The problem is that these images don't load. Instead the text above is displayed. The
strange thing is that you cannot select the text, but if I right-click on it, I get a
contextual menu with the options "View Image", "Copy Image", etc. So
it seems the files are recognized as images. Bitmap images in file formats like PNG do
load directly. Does anyone on the list know what I need to do to make SVGs load directly
too?
Cheers,
Pi
---------------------------------------------------------------
Biomolecular Mass Spectrometry & Proteomics group
Utrecht University
Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands
Mail address:
P.O. box 80.082
3508 TB Utrecht
The Netherlands
phone: +31 6 143 66 783
email: pieter.neerincx(a)gmail.com
skype: pieter.online
---------------------------------------------------------------
4:11 p.m.
New subject: SVG images in tool.xml don't load (Fixed)
Hi,
This drove me nuts for a while, but I found a solution. In case anyone else wants to add
SVG images the help section here is a workaround:
Apparently reStructuredText is part of a package called Docutils. The current
"stable" version of Docutils does not support SVG images. SVGs need to be placed
in an <object> tag, but Docutils generates HTML with the svg in an <image>
tag. This is fixed in the development version. If you don't want the unstable version,
you can use something like the code below to insert raw html code into the help section.
Note that the examples for inserting raw html in the Docutils documentation are not
correct: you'll need to encode the < and > characters.
-----------------------------------
.. role:: raw-html(raw)
:format: html
.. class:: infomark
**What it does**
Some help on how to use this great tool.
:raw-html:`<object data="/images/custom_galaxy_tools/myTool.svg"
type="image/svg+xml" width="100%"/>`
Some more help on how to use his tool
-----------------------------------
Also note that the raw-html role must be at the beginning of the reStructuredText
preceding any other directives.
Cheers,
Pi
On Apr 13, 2010, at 11:22 AM, Pieter Neerincx wrote:
Hi,
I have some tools that produce SVG images. These load just fine in a browser when they
are in the middle part of a galaxy browser window as tool output. But now I've added
some example images as documentation in the help section of the *.xml tool config files
using the reStructuredText syntax like this:
.. image:: /images/custom_galaxy_tools/ExtractModificationSiteSequenceContext.svg
The problem is that these images don't load. Instead the text above is displayed. The
strange thing is that you cannot select the text, but if I right-click on it, I get a
contextual menu with the options "View Image", "Copy Image", etc. So
it seems the files are recognized as images. Bitmap images in file formats like PNG do
load directly. Does anyone on the list know what I need to do to make SVGs load directly
too?
Cheers,
Pi
---------------------------------------------------------------
Biomolecular Mass Spectrometry & Proteomics group
Utrecht University
Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands
Mail address:
P.O. box 80.082
3508 TB Utrecht
The Netherlands
phone: +31 6 143 66 783
email: pieter.neerincx(a)gmail.com
skype: pieter.online
---------------------------------------------------------------
-------------------------------------------------------------
mobile: +31 6 143 66 783
e-mail: pieter.neerincx(a)gmail.com
skype: pieter.online
-------------------------------------------------------------
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galaxy-user@lists.galaxyproject.org
6 comments
4 participants
participants (4)
-
Andreas Kuntzagk -
Assaf Gordon -
Nate Coraor -
Pieter Neerincx