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Question: MACS2 predictd error on Galaxy CloudMan
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gravatar for alishamassa
13 months ago by
alishamassa • 20
alishamassa • 20 wrote:

Hello,

I just got to ChIP-seq peak calling in my Galaxy CloudMan instance. The MACS2 predictd tool appears to be an older version with a known issue the tool version in CloudMan is 2.1.0.20151222.0 See this thread here for this known issue https://biostar.usegalaxy.org/p/23364/ The error I receive when I try this repeatedly is "Fatal error: cannot open file 'predictd': No such file or directory"

Looks like I need this version 2.1.1.20160309.0 of the MACS2 predictd tool which is corrected for this known issue.

Any ideas how to get this (in simple terms I am very bad with computers, hence using the amazing Galaxy CloudMan) without using ssh command line?

Thank you
cloud cloudman chip-seq • 438 views
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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by alishamassa • 20
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

New tools can be added to your Cloudman instance through the Admin tab of the Galaxy application.

To become an admin inside of the Galaxy application, there are two required steps:

  • add your registered account's email address to the list of server admins on Cloudman's cloud/admin form
  • create a registered account using that same email address (if you haven't already) in the Galaxy application

Now, when logged into the instance, a new tab for Admin will appear in the masthead. Click into that to manage local data, add tools, and do other admin tasks the same as one would with a local Galaxy instance: https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/.

All of this is GUI based (not line command).

Hope that helps! Jen, Galaxy team
ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thanks so much Jen, worked perfectly!

ADD REPLY • link written 13 months ago by alishamassa • 20
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