Question: Problem with toolshed installed deepTools on CloudMan instance
gravatar for Marco Blanchette
4.5 years ago by
United States
Marco Blanchette10 wrote:

I successfully installed deepTools using the toolShed from the Galaxy main repos. The problem is that when users try to do analysis with deepTools, they always get the following message: 

ERROR: Unable to read builds for site file /mnt/galaxy/galaxy-app/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt

Incidentally, this is the same message I get after successfully downloading genomes from UCSC using dataManagers.

Could someone shed some lights on how to fix this issue?



software error galaxy cloudman • 1.0k views
ADD COMMENTlink modified 4.5 years ago by Jennifer Hillman Jackson25k • written 4.5 years ago by Marco Blanchette10

Hi Marco,

can you check if the file /mnt/galaxy/tool-data/shared/ucsc/ucsc_build_sites.txt exists? It seems to be a Galaxy problem with reference genomes and not deepTools related.

ADD REPLYlink written 4.5 years ago by Bjoern Gruening5.1k

You probably meant to say /mnt/galaxy/galaxy-app/tool-data/shared/ucsc/ucsc_build_sites.txt, right? 

In fact, on the CloudMan instance there is none... there is 




But no .txt file... Is your suggestion to make one of them the txt file?

ADD REPLYlink written 4.5 years ago by Marco Blanchette10
gravatar for Jennifer Hillman Jackson
4.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Marco,

From our earlier testing, starting up Cloudman creates this file. However, if you have a custom start-up script, custom version of this file, or are not using the latest ami for some reason, then you may need to create the file. Full details are now highlighted in the recent News Brief here (this was included/introduced earlier, but we have linked in more detail to aid administrators):

Hopefully you can solved the problem by now, but if not, this helps to do that,

Take care, Jen, Galaxy team

ADD COMMENTlink written 4.5 years ago by Jennifer Hillman Jackson25k
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