Question: Problem installing fastq groomer from ToolShed on CloudMan instance
0
gravatar for Marco Blanchette
4.5 years ago by
United States
Marco Blanchette10 wrote:

Dear all,

I've been trying to install tools on my brand new CloudMan Galaxy instance using toolshed. I am trying to install Fastq Groomer and I am getting errors related to galaxy_sequence_utils. Am'I doing something wrong? Here is the error log from that dependency from the admin tool management panel:

 

Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz
Extracting in /mnt/galaxy/tmp/tmpEGkh_V
Now working in /mnt/galaxy/tmp/tmpEGkh_V/distribute-0.6.38
Building a Distribute egg in /mnt/galaxy/tmp/tmp-toolshed-mtd63TIJa/galaxy_sequence_utils-1.0.0
/mnt/galaxy/tmp/tmp-toolshed-mtd63TIJa/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg
error: /usr/local/lib/python2.7/dist-packages/distribute-0.7.3-py2.7.egg/site.py: No such file or directory

 

 

Thanks a bunch

tools galaxy cloudman • 1.7k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Marco Blanchette10

How did you launch this CloudMan instance?  I've just launched a new one and have installed Fastq Groomer successfully without seeing this issue.

ADD REPLYlink written 4.5 years ago by Dannon Baker3.7k

Same for me... Still trying to figure out what's wrong with the other instance...

One issue though... I was unable to specify a new panel section on either the new or the old instances. For examples, I couldn't put the bedtools in a bedtools section, everything appear at the end of the menu (also, I couldn't figure out the XML config file (or else) specifying where these should be located (weird because I was able to add the NGS.plot tool to the tools_config.xml and have them display correctly...) I must be missing how the side panel is fully populated...

Just let me know if you have a sense if what's going on (I'm going through the different tools that need update right now hopping to fix the initial issue)

Thanks

ADD REPLYlink written 4.5 years ago by Marco Blanchette10
1
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Marco,

can you check if you python-distribute package is working properly or is installed? It does not seem like a Galaxy issue, more a general python issue.

Cheers,

Bjoern

ADD COMMENTlink written 4.5 years ago by Bjoern Gruening5.1k
0
gravatar for Marco Blanchette
4.5 years ago by
United States
Marco Blanchette10 wrote:

Hmm... I'm a bit clueless as what is going on... Python is working fine, running version 2.7.3. I'm not a python person so i can't really easily test anything... But I did restart the server and now I'm getting a different error

 

Tool dependency status:Error

Tool dependency installation error:This tool dependency's required tool dependency galaxy_sequence_utils version 1.0.0 has status Error.

 

Also, I am running on revision 13084:cc0fe62e54dc, if this help. I'm about to start a new server and test if it breaks...

ADD COMMENTlink written 4.5 years ago by Marco Blanchette10
1

Can you check your dependencies in your Admin panel and 'repair' all missing dependencies?

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