Repeat Explorer

admin

#1

Hi
I’m trying to install Repeat Explorer under a local Galaxy. I run what is described here:

http://repeatexplorer.umbr.cas.cz/static/html/help/manual.html#adding-repeatexplorer-to-your-local-galaxy-installation

I don’t use the batch, but I did all the stuff indicated, but I have some questions.

In the main directory, there is not a “tool_conf.xml” file. It is in the Config directory, but there is a main and a sample files. Well, I tryied to change both, but nothing happens. I did only change a name in the files, just for see if the changes are working, but nothing.

What am I doing wrong?
Thanks in advance!
Rubens.


#2

After you set up all the dependencies for the repeat explorer (which seems to be described here you should add the tools to your Galaxy like this:
In your Galaxy make a copy of tool_conf.xml.sample naming it tool_conf.xml, then add the contents of tool.xml from the repeatexplorer repo. Restart Galaxy.

There also seems to be a newer version of that repo: https://bitbucket.org/petrnovak/repex_tarean


#3

Thank you, Marten!

I tested the tool_conf.xml file changing only a description name of “get data”, just to check it out if the configuration is ok. It doesn’t work, there is no change in the tools list. Everything else about Repeat Explorer I have done.

Cheers,
Rubens.


#4

Did you restart your Galaxy after you created the file? Did you change the default location of that file in the configuration?


#5

Yes, I restarted many times. I don’t change the location.


#6

try removing an entry from that file and see if it disappears in your Galaxy toolpanel


#7

I did it. The “get data” stays there with only an application I’ve instaled after. Put it on again, and everything is fine. Paste Repeat Explorer and voilá…

Thank you for now…

If I could disturb you a little more, I upload an SRA file and run fastq-dump. I received an error message

home/pasa/galaxy/database/jobs_directory/000/10/tool_script.sh: linha 9: /Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump: Arquivo ou diretório não encontrado (file or directory not found)

Thanks!


SRA file and run fastq-dump error on local Galaxy
#8

Note: moderator created “New Topic” linked to this post for the new question. Follow-up should go there.

How to create new linked topics:


#9

Thank you!