Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool
standard output (stdout)? On my system
only the last five lines of tool output are shown there.
2.) Currently I get the message This dataset is large and only the
first
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool
standard output (stdout)? On my system
only the last five lines of tool output are shown there.
The
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool
standard output (stdout)? On my system
only the last five lines
On Tue, Jul 23, 2013 at 2:12 PM, Gromobir gromo...@arcor.de wrote:
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir gromo...@arcor.de wrote:
Hello Peter,
Thanks a lot for your reply. I was talking about the stdout, which can be
displayed after clicking on the i icon.
I went to i-icon - stdout and only the last five lines are displayed
there.
Hmm. Which tool (or
Hi,
I work myself through the job_conf.xml and have a question:
a)
In your advanced example you have:
destination id=remote_cluster runner=drmaa tags=longjobs/
destination id=real_user_cluster runner=drmaa
!-- TODO: The real user options should maybe not be considered
runner
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed in the tool
standard output (stdout)? On my system
only the last five lines of tool output are shown there.
2.)
On 07/23/2013 03:47 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir gromo...@arcor.de wrote:
Hello Peter,
Thanks a lot for your reply. I was talking about the stdout, which can be
displayed after clicking on the i icon.
I went to i-icon - stdout and only the last five lines are
On 07/23/2013 04:05 PM, Peter Cock wrote:
2.) Currently I get the message This dataset is large and only the first
megabyte is shown below every time
I try to display a file, which is larger than one megabyte. Is it possible
to change this size, such that I won't get this
message anymore for
I am launching a brand new instance of the latest AMI. The volume specified in
the log does not exist in my account. I was under the impression that the AMI
should create this volume for me?
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Monday, July 22, 2013
On 07/23/2013 03:17 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 2:12 PM, Gromobir gromo...@arcor.de wrote:
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to
Hello,
It seems you are right. It has nothing to do with the SQLAlchemy. I checked
the Galaxy log and didn't find any other error log. After upgrading the
database to MySQL when I uploaded the first input file, job dispatched to
local runner and everything was fine. But when I tried to upload
1. Thanks, I'll try this out, after you reavealed me which version I should
use :)
2. Originally I had this workflow to start with
https://main.g2.bx.psu.edu/u/mj--/w/ngs
, but I at the sam-to-bam conversion I get the sequences are not currently
available for specified build error when using
Hi galaxy-dev,
I have a tool that generates a HTML output file which uses some javascript
library. I cannot view the output file with the eye button in Galaxy, but it
still works fine from the HTML file opened out of the file directory.
I changed the sanitize_all_html = False and restarted the
On 07/23/2013 05:14 PM, Sinthong, Phanwadee wrote:
Hi galaxy-dev,
I have a tool that generates a HTML output file which uses some javascript
library. I cannot view the output file with the eye button in Galaxy, but it
still works fine from the HTML file opened out of the file directory.
I
Hi Gred,
I'm trying to update this repository (initially just to switch my
README file to reStructuredText as the current plain text is
not being rendered nicely):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
Uploading my new tar-ball failed:
Internal Server Error
Galaxy was
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Björn,
This one has been applied in changeset 10219:a7edac403b6c, and all of
your patches are now running on the test tool shed.
Thanks very much,
Greg Von Kuster
Hi Greg Björn,
I think supporting
On Tue, Jul 23, 2013 at 5:20 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Gred,
I'm trying to update this repository (initially just to switch my
README file to reStructuredText as the current plain text is
not being rendered nicely):
I'm using JQuery with files *.js extension. I tried adding the data type as you
suggested but it still doesn't seem to fix the problem.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Gromobir
Was stuck up with my approach of wrapping the Workflows in a toolbox
and hence this blog post is a bit delayed.
http://galaxy-gsoc2013.blogspot.in/2013/07/week-5-update.html
Saket
___
Please keep all replies on the list by using reply all
Hi Galaxy dev team,
I'm trying to the you galaxy server to do NGS peak calling: Tools - NGS: Peak
Calling -
MACShttps://main.g2.bx.psu.edu/tool_runner?tool_id=peakcalling_macs
Model-based Analysis of ChIP-Seq. However, the page won't allow me enter the
input files: the drop-down selection box
Hi- while I was able to solve the share string problem, the share string
has stopped working again. In addition, I am unable to increase disk size
either through the CloudMan console or a dialog box that appears before the
cloudman console. Below are the cluster status logs. The Disk status
Björn,
I've uploaded the modified tool_dependencies.xml to devteam's
package_emboss_5_0_0 repository on the test tool shed, and verified that
it works. Again, thank you for your contributions.
--Dave B.
On 7/7/13 18:59:57.000, Björn Grüning wrote:
Hi Greg,
bitbucket has a downtime so I
Hi Dave,
Björn,
I've uploaded the modified tool_dependencies.xml to devteam's
package_emboss_5_0_0 repository on the test tool shed, and verified that
it works. Again, thank you for your contributions.
Great, thanks!
--Dave B.
On 7/7/13 18:59:57.000, Björn Grüning wrote:
Hi
Hey, thanks for the response.
The ssh issue was on my end and is now resolved.
However, when I try the old AMI (ami-da58aab3), it mounts the new directory
structure (meaning galaxyTools does not exist). Why does the old AMI have the
directory structure of the new AMI?
Along with that,
Nevermind, this issue was resolved once I fixed my issue with ssh'ing into
outside hosts.
Thanks.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent: Tuesday, July 23, 2013
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