Tool Dependency Check for eXpress - requirements syntax incorrect?
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/ aebrenne@uci.edu
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 <aebrenne@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/ aebrenne@uci.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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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-re... -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/ aebrenne@uci.edu On Thu, Jun 27, 2013 at 11:03 AM, James Taylor <james@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 <aebrenne@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/ aebrenne@uci.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Adam Brenner -
James Taylor