Hi all,
I am a little confused as to the right way to configure my installed NGS tools.
From the documentation I've found and from looking at the xml/python
wrappers, it looks to me like the NGS tool wrappers simply call the tools and assume they will be in the galaxy account's PATH. For instance, bwa_wrapper.py simply calls "bwa" in the shell. So it looks to me like the default assumption is that bwa was installed as root and is available to all users, and will always be on your PATH. Is this right, or am I missing some configuration options that should tell galaxy where to find the bwa binary?
If this is the case, what is the best way to install and maintain two versions of the same tool? I can write code into the wrapper to find the correct version of the tool in a given case, but I was wondering if there is a more standard 'galaxy' way to configure this.
Sorry for the newbie questions again - I have been looking at the NGS setup and Tools documentation, but I don't think I've found anything on multiple installed versions of a tool. Also if there are any docs I have missed on configuring path environment variables, please let me know!
Thanks, Clare