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.
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.
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.
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)