James,

Thanks for the response. I had some sort of typo in my
express_wrapper.xml file and all is well now. It is now sourcing the
correct file. I went ahead and submitted a pull request to have
eXpress updated to package, instead of binary:
https://bitbucket.org/galaxy/galaxy-central/pull-request/192/express-tool-requirements-tag-updated/diff

-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Thu, Jun 27, 2013 at 11:03 AM, James Taylor <ja...@jamestaylor.org> wrote:
> Hi Adam, yes, it should be package, the "binary" type has never been
> supported but keeps getting propagated for some reason. At some point
> it might be nice to have a configurable mapping from the other
> dependency types to packages.
>
> However, changing it to package *should* work. Can you send the
> relevant part of the paster log, it should log information about
> dependency resolution and the command line.
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Thu, Jun 27, 2013 at 1:38 PM, Adam Brenner <aebre...@uci.edu> wrote:
>> Howdy,
>>
>> One of our users is running the eXpress package under NGS: RNA
>> Analysis -> eXpress -- galaxy/dist/tools/ngs_rna/express_wrapper.*
>>
>> I noticed the syntax for express_wrapper.xml has the following:
>>      <requirement type="binary">eXpress</requirement>
>> any reason why it was set to that, as opposed to:
>>      <requirement type="package">eXpress</requirement>
>>
>> In our setup, we need to source the env.sh file for express to setup
>> the correct environmental variables. Changing from binary to package
>> has not solved this and re-running the job never sources our env.sh
>> file.
>>
>> What am I doing wrong?
>>
>> My tool dependency directory looks like so:
>>    galaxy/dist/tool_dependency/eXpress/
>>    |---default --> 1.3.0
>>    |----1.3.0/env.sh
>>
>> Thanks,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> aebre...@uci.edu
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