Clare, it would be great if you can contribute these back. We have't gone 
through and added these everywhere yet. Pull requests in bitbucket would be 
easiest. Thanks!



On Nov 16, 2011, at 9:29 PM, Clare Sloggett <s...@unimelb.edu.au> wrote:

> Hi James & all,
> 
> I have been getting some errors to do with the path environment
> variable. For instance, when uploading a sam file to our local galaxy
> instance, we got:
> "Traceback (most recent call last):
> File "/data/ugalaxy/galaxy-dist/tools/data_source/upload.py", line 394, in
>   __main__()
> .....
> line 63, in _get_samtools_version
>   output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
> File "/usr/local/lib/python2.7/subprocess.py", line 679, in __init__
>   errread, errwrite)
> File "/usr/local/lib/python2.7/subprocess.py", line 1228, in _execute_child
>   raise child_exception
> OSError: [Errno 2] No such file or directory"
> 
> I can post the full error if you'd like, but basically the problem was
> that samtools wasn't in the PATH. This was because we have our tools
> installed in a non-standard place, so we are depending on the
> requirements being specified as James described below, and samtools
> isn't specified as a requirement in upload.xml, so when upload.py
> calls datatypes.py and tries to use samtools, it gives an error. I've
> found a couple of other examples like this - for instance samtools is
> also used by some picard scripts so should be specified as a
> requirement in the picard wrappers.
> 
> These problems probably don't show up in most cases when people just
> have the tools installed as root and on their PATH by default?
> 
> I'm going to be fixing these where I find them. Would it be helpful
> for me to contribute these tweaks back or would it be better just to
> raise an issue?
> 
> Thanks,
> Clare
> 
> On Wed, Nov 16, 2011 at 4:33 PM, Clare Sloggett <s...@unimelb.edu.au> wrote:
>> 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_dependency_dir%29
>> .
>> 
>> 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 <s...@unimelb.edu.au> wrote:
>>> Great! Thanks James, this is exactly what I need.
>>> 
>>> On Wed, Nov 16, 2011 at 2:20 PM, James Taylor <ja...@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: s...@unimelb.edu.au
>>> P: 03 903 53357
>>> M: 0414 854 759
>>> 
>> 
>> 
>> 
>> --
>> E: s...@unimelb.edu.au
>> P: 03 903 53357
>> M: 0414 854 759
>> 
> 
> 
> 
> -- 
> E: s...@unimelb.edu.au
> P: 03 903 53357
> M: 0414 854 759

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