Hi Nate,
thanks for your reply. My solution will break down in such a case, indeed. So
here is what I need/have:
I have a tool which allows the user to select a specific workflow and
appropriate input data from his/her
history. On execution a script is used to do several preprocessing
Hi everyone,
my local installation of Galaxy has an issue with using the Upload File tool
on data that was uploaded to the ftp server. The ftp upload itself works fine:
-rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa
but there seems to be some issue with Galaxy moving it and I have
So, I fixed the problem myself ;-). For whatever reason the files need to be
owned by the galaxy user. I achieved that by setting
SQLDefaultUID 501
SQLDefaultGID 501
in the proftpd.conf. 501 is the UID and GID of the galaxy user and group.
- Original Message -
From: Sarah Diehl
Excuses for the repost, but I really need to solve this.
Uploading with FTP fails on our Galaxy, because the /tmp directory has
not enough space. How can I hack in the Galaxy code base that the
temporary directory needs to be /mnt/galaxydb/tmp ? Another solution:
how can I provide a symlink
Yes:) I meant to do it algorithmically though from within the code of the
tool or the xml wrapper:)
On Wed, Aug 15, 2012 at 7:10 PM, Ross ross.laza...@gmail.com wrote:
Does clicking the info (i) icon on a history item help?
On Wed, Aug 15, 2012 at 7:16 AM, Robert Chase
On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote:
Excuses for the repost, but I really need to solve this.
Uploading with FTP fails on our Galaxy, because the /tmp directory has not
enough space. How can I hack in the Galaxy code base that the temporary
directory needs to be
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote:
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like it doesn't do what I would like.
I want to create a tool that allows the user to upload a data file and
then have it run through one or more filters. Each filter
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote:
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like it doesn't do what I would like.
I want to create a tool that allows the
Hello all,
I have a set of galaxyised R scripts, called directly via 'Rscript',
which I run in workflows for microarray analysis.
I would like to collect the parameters used at each step, for report
generation, re-runs and provenance. My Galaxy noob instincts tell me to
have each script
On Thu, Aug 16, 2012 at 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote:
Hi all,
I'm trying to wrap my head around what the conditional tag does...it
looks like
On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
Hello Dan,
The easiest way to go about this, since you said that none of your
filters are mutually exclusive, is to use the select
Hi
I'm writing a tools for an executable that writes results to stdout and reports
success message to stderr, so it really need the improved error handling. Is
there any sample code or documentation available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
On 08/16/2012 03:02 PM, Birgit Crain wrote:
Hi
I'm writing a tools for an executable that writes results to stdout
and reports success message to stderr, so it really need the improved
error handling. Is there any sample code or documentation available?
Thanks
*Birgit Crain, Ph.D.*| Sr.
On Thu, Aug 16, 2012 at 8:02 PM, Birgit Crain
bcr...@completegenomics.com wrote:
Hi
I'm writing a tools for an executable that writes results to stdout and
reports success message to stderr, so it really need the improved error
handling. Is there any sample code or documentation available?
No, I call the executable directly from the xml. It kept failing although it
seemed to finish the job and I realized that on success the executable prints a
summary message to stderror, because it's using stdout for the actual results
so they can be pipped to another command.
From the July news
On 8/8/12 4:06 PM, Nate Coraor n...@bx.psu.edu wrote:
On Aug 8, 2012, at 2:30 PM, Karger, Amir wrote:
Meanwhile, we're able to restart, and get happy log messages from the
jobrunner and two web servers (two servers running on different ports
of a Tomcat host). And I can do an upload, which
Hi John and Peter,
On Thu, Aug 16, 2012 at 11:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hi John,
On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote:
Hello Dan,
The easiest way to go
To Galaxy,
I installed Galaxy on my local server..
I modified the universe_wsgi.ini file as follows:
# The address on which to listen. By default, only listen to localhost (Galaxy
# will not be accessible over the network). Use '0.0.0.0' to listen on all
# available network interfaces.
host =
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