User: Nicholas.Blackburn

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Posts by Nicholas.Blackburn

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Comment: C: Getting tophat2 ref index when using data_managers
... Sorry - I can't offer any advice, hopefully Jennifer or another Galaxy project person will respond to you. ...
written 19 months ago by Nicholas.Blackburn140
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Comment: C: Getting tophat2 ref index when using data_managers
... Hi Jennifer, I think biowz still needs help with this. Are you guys going to offer some suggestions / details / answers? ...
written 19 months ago by Nicholas.Blackburn140
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Comment: C: Getting tophat2 ref index when using data_managers
... Assuming you have a file /galaxy in the top directory and that you've generated a bowtie2 index using the data_manager tools (so you should be able to see a reference genome when you look at the bowtie2 tool in galaxy) just do as one line: tail -n 2 /galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/de ...
written 19 months ago by Nicholas.Blackburn140
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Comment: C: Could someone please send me or link me to https://usegalaxy.org's shed_tool_con
... Evidently not as simple as replacing mine with these. Damn, but thank you!  ...
written 20 months ago by Nicholas.Blackburn140
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Could someone please send me or link me to https://usegalaxy.org's shed_tool_conf.xml file?
... I need to arrange the tools in the tool panel of my local instance and I don't have hours to spend shuffling around sections in the shed_tool_conf.xml file. (would be good if there was a GUI way to do this!!). So if someone has access to the https://usegalaxy.org shed_tool_conf.xml could they pleas ...
galaxy tool panel written 20 months ago by Nicholas.Blackburn140 • updated 20 months ago by Martin Čech ♦♦ 3.7k
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Getting tophat2 ref index when using data_managers
... While setting up a local galaxy instance despite having generated a bowtie2 index using the data_manager tools, and having my reference genome appear in the bowtie2 tool reference genome dropdown, it wasn't appearing in the tophat2 tool reference dropdown. Even though the bowtie2 reference index is ...
bowtie2 galaxy data_managers tophat2 written 20 months ago by Nicholas.Blackburn140 • updated 19 months ago by Jennifer Hillman Jackson21k
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Comment: C: Reference genome download - a step-by-step please?
... Hi Jen, Our sysadmin set up a fair bit and he's finished with us for now so I can guess a bit based on what I know.  - Local instance - recent clone from github, latest release - and we got tools in a roundabout way following details you linked us to here If there's any system stats I can pull out ...
written 21 months ago by Nicholas.Blackburn140
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Comment: C: Reference genome download - a step-by-step please?
... Note to anyone else who reads this thread: watch the tutorial video at this link - extremely helpful. ...
written 21 months ago by Nicholas.Blackburn140
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Comment: C: Reference genome download - a step-by-step please?
... The video tutorial was instrumental for me to understand the process. Particularly the whole hidden admin history, finding that out with the video was a game changer. However that said I had to reboot my galaxy instance each time a data_manager tool was installed, and then again when an index had b ...
written 21 months ago by Nicholas.Blackburn140
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Comment: C: Reference genome download - a step-by-step please?
... Hi, thanks for getting back to me. I've read that link and several others and am still thoroughly confused. I really need a step-by-step guide as I explained above.  ...
written 21 months ago by Nicholas.Blackburn140

Latest awards to Nicholas.Blackburn

Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Getting tophat2 ref index when using data_managers
Appreciated 19 months ago, created a post with more than 5 votes. For Getting tophat2 ref index when using data_managers
Student 19 months ago, asked a question with at least 3 up-votes. For Reference genome download - a step-by-step please?
Student 21 months ago, asked a question with at least 3 up-votes. For Reference genome download - a step-by-step please?

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