User: bankapur

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bankapur0
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Posts by bankapur

<prev • 15 results • page 1 of 2 • next >
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Comment: C: HTML page output in history - no css gets loaded
... Hi Dannon, Thank you for your reply. I couldn't find "Manage Display Whitelist" under Galaxy admin panel however I switched the following settings in galaxy.ini file: sanitize_all_html = False serve_xss_vulnerable_mimetypes = True This helped in getting the proper css to load, however the JS ass ...
written 23 months ago by bankapur0
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HTML page output in history - no css gets loaded
... Hello, My pipeline produces an html report with links to other html pages. I have integrated this report into my galaxy instance as a tool output using the following information: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Use_an_html_output_file However the css involved ...
history html written 23 months ago by bankapur0 • updated 23 months ago by Dannon Baker3.7k
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Comment: C: set_environment fails to set up Trinity path
... I have a galaxy instance installed on a remote server. The ultimate goal is to run Trinity (which is also located on the server). My bashrc includes the path to Trinity called "TRINITY_HOME", which I use in the trinityrnaseq.xml in the requirement tag and set type="set_environment". Error being "Tri ...
written 2.7 years ago by bankapur0
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Comment: C: set_environment fails to set up Trinity path
... The second point in my post is where I state that I use tool_dependencies.xml. my understanding of galaxy is that it uses the user's bashrc file to run tools. However, it doesn't do so for me. Is this a permissions issue?  ...
written 2.7 years ago by bankapur0
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set_environment fails to set up Trinity path
... I have a local galaxy instance on which I am trying to run Trinity. I have the following in my bashrc: export TRINITY_HOME=/../../SOFTWARE/trinityrnaseq I have tried to use this in three ways: 1) Included TRINITY_HOME in requirement type but this fails. I don't understand why, as Trinity is loade ...
galaxy written 2.7 years ago by bankapur0
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Comment: C: TypeError while executing sh run.sh
... This was my fault, I think something got edited accidentally in the eggs.ini file when I switched to fresh copy of eggs.ini everything went back to normal.  ...
written 2.7 years ago by bankapur0
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(Closed) TypeError while executing sh run.sh
... I am trying to run my galaxy instance off of a remote server and when I execute sh run.sh, I get the following error: tool_shed.tool_shed_registry DEBUG 2015-05-15 14:12:46,792 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample tool_shed.tool_shed_registry DEBUG 2015-05-15 1 ...
galaxy written 2.7 years ago by bankapur0
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Comment: C: Tools integrated into a pipeline not working on a galaxy instance
... I did a chmod 777 on the directory I wanted galaxy to write files to for the meantime. I will configure the job_working_directory in galaxy.ini file from now on. Thank you Nate! ...
written 2.7 years ago by bankapur0
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Tools integrated into a pipeline not working on a galaxy instance
... Hi, I am trying to integrate my own tool into galaxy on a remote server (LSF). I have made myself admin on the instance and work from there. This pipeline runs Trimmomatic, Tophat, Cufflinks, Cufflinks Annotation (and many more).  I started out small and ran Trimmomatic alone and it failed with a: ...
lsf local config tools rna-seq written 2.7 years ago by bankapur0 • updated 2.7 years ago by Nate Coraor3.1k
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Comment: C: No case matched value Error with use of conditional statements
... I have edited my original post to include the entire xml file at this point. Let me know if you find error in the way the command line is constructed. ...
written 2.7 years ago by bankapur0

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