User: CMonger

gravatar for CMonger
CMonger0
Reputation:
0
Status:
New User
Location:
Ireland
Website:
https://github.com/cmo...
Last seen:
3 years, 3 months ago
Joined:
3 years, 6 months ago
Email:
c**************@gmail.com

Genetics biologist turned bioinformatics PhD Student based in Ireland.

I am currently developing a Galaxy server for RNA-Seq experiments for internal use.

Posts by CMonger

<prev • 8 results • page 1 of 1 • next >
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How can I order tools in the toolbar on a local Galaxy instance?
... Hi all, I've searched the wiki and looked for similar questions on biostars but cannot find the answer to this anywhere. What files needs to be configured (and what tags need to be used) to assign tools into categories?  For example, I mean the header "NGS Toolbox BETA" on main as well as the sub- ...
galaxy written 3.5 years ago by CMonger0 • updated 3.5 years ago by Matthias Blum30
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Comment: C: Cannot get scripts to show in Galaxy
... My apologies, just realized my xml was invalid. Fixed the syntax error and its now showing up. Thanks for pointing me to the cause of the problem! ...
written 3.6 years ago by CMonger0
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Cannot get scripts to show in Galaxy
... Hi all, I've been attempting to create and integrate a script into Galaxy using instructions in various tutorials and the official wiki but have yet to successfully do so. I've placed the python script and an xml wrapper in /pathtogalaxy/tools/myTools/ and updated the config/tool_conf.xml file wit ...
galaxy software error written 3.6 years ago by CMonger0 • updated 3.6 years ago by Martin Čech ♦♦ 4.9k
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Comment: C: Cannot get Galaxy to run on workstation
... Hi Martin, thanks again for more advice. As suggested in the first link, I checked my python path within the galaxy environment and it contained the path to the python modules (I specifically edited this to include a direct path to both expat and element tree in the /pathtopython/xml/etree/ and /pa ...
written 3.6 years ago by CMonger0
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Comment: C: Cannot get Galaxy to run on workstation
... Is there any additional information I could provide to try and figure out the root of the problem?  ...
written 3.6 years ago by CMonger0
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Comment: C: Cannot get Galaxy to run on workstation
... This was done in a virtualenv created as described here ...
written 3.6 years ago by CMonger0
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Comment: C: Cannot get Galaxy to run on workstation
... Hi Jen, thanks for the quick response. I deleted Python2.6 to avoid confusion between the 2 versions and changed the path as follows: galaxy@bioinfo-wstation-01:~/galaxy$ export PYTHONPATH="/usr/bin/python2.7/:/usr/lib/python2.7/:/usr/lib/python2.7/xml/parsers/expat.py" galaxy@bioinfo-wstation-01: ...
written 3.6 years ago by CMonger0
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Cannot get Galaxy to run on workstation
... Hi all, I'm having some trouble setting up a Galaxy instance on our workstation (which I ssh into).  I have created a user specifically for Galaxy as described in the installation documents but am having trouble getting it to work. When using run.sh to start up the server I get this error (pastebi ...
galaxy written 3.6 years ago by CMonger0

Latest awards to CMonger

Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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