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
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
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.
You should provide "tool_dependency_dir" in the config file and point it at some directory $SW where you will install tools under.
With this enabled, when a tool has a dependency, Galaxy will look for it under that directory and attempt to run a script to setup the environment. For example if you have tool with a dependency on foo version 1.3, Galaxy will look for:
$SW/foo/1.3/env.sh
and if found will source it as part of the job submission script. This usually contains something simple like
PATH=$PACKAGE_BASE/bin:$PATH
to add the binaries installed with the dependency to the path.
Ideally all dependencies used by Galaxy tools would be installed in this way.
Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor james@jamestaylor.org wrote:
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
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.
You should provide "tool_dependency_dir" in the config file and point it at some directory $SW where you will install tools under.
With this enabled, when a tool has a dependency, Galaxy will look for it under that directory and attempt to run a script to setup the environment. For example if you have tool with a dependency on foo version 1.3, Galaxy will look for:
$SW/foo/1.3/env.sh
and if found will source it as part of the job submission script. This usually contains something simple like
PATH=$PACKAGE_BASE/bin:$PATH
to add the binaries installed with the dependency to the path.
Ideally all dependencies used by Galaxy tools would be installed in this way.
Looks like it's working! The problem I had run into, in hindsight, was a) I hadn't set tool_dependency_dir as I didn't know about it b) if I had set it, I was installing tools to $SW/tool-name/version-number/ but the default tool wrappers in galaxy-dist don't have version numbers set, so they will just look in $SW/tool-name/ .
Can I suggest this be added to the wiki somewhere under the Admin pages? Apologies if it's there, I couldn't find it except under News Briefs at http://wiki.g2.bx.psu.edu/News%20Briefs/2010_11_24?highlight=%28tool_depende... .
As well as being on the wiki it would be useful to have it (commented out by default) in universe_wsgi.ini. I think the tool_dependency_dir variable isn't in there at all at the moment, at least in the galaxy-dist I have. It would also be useful to have a brief mention or link to it on http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup to save time for people like me who had tools installed in a non-standard place.
Thanks again! Clare
On Wed, Nov 16, 2011 at 3:01 PM, Clare Sloggett sloc@unimelb.edu.au wrote:
Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor james@jamestaylor.org wrote:
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
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.
You should provide "tool_dependency_dir" in the config file and point it at some directory $SW where you will install tools under.
With this enabled, when a tool has a dependency, Galaxy will look for it under that directory and attempt to run a script to setup the environment. For example if you have tool with a dependency on foo version 1.3, Galaxy will look for:
$SW/foo/1.3/env.sh
and if found will source it as part of the job submission script. This usually contains something simple like
PATH=$PACKAGE_BASE/bin:$PATH
to add the binaries installed with the dependency to the path.
Ideally all dependencies used by Galaxy tools would be installed in this way.
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
galaxy-dev@lists.galaxyproject.org
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Clare Sloggett -
James Taylor