Re: [galaxy-dev] writing command tag in xml file for a C++ tool

Hi VJ, bedtools is not new. It is in already available through the toolshed. Here are a few relevant links: http://wiki.galaxyproject.org/Tool%20Shed http://testtoolshed.g2.bx.psu.edu/view/bgruening/bedtools_test_bag Furthermore, the bedtool maintainer offers wrappers from his main website.

[galaxy-dev] Suggestion for Latest revision: installation errors

Hi Greg, I think it would be useful to be a little more inclusive on the Tool Shed listing Latest revision: installation errors and include repositories with tools missing tests, e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180 Some of the BLAST+ tools don't yet

Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

On Wed, May 22, 2013 at 9:59 PM, Greg Von Kuster g...@bx.psu.edu wrote: I cannot guarantee it, but this may be related to a fix I just committed that populates the repository tag in the dependency definitions with a toolshed attribute if it is missing (it looks like it is in your case). I

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

Hello Nate, On May 14, 2013, at 10:58 AM, John Chilton wrote: Hey Nate, On Tue, May 14, 2013 at 8:40 AM, Nate Coraor n...@bx.psu.edu wrote: Hi John, A few of us in the lab here at Penn State actually discussed automatic creation of virtualenvs for dependency installations a

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

For the first of the CloudMap workflows that worked. But the second failes with this error message: Failed to open URL: https://main.g2.bx.psu.edu/workflow/export_to_file?id=f444ce954bdc4953 Exception: HTTP Error 500: Internal Server Error I don't see any information in the log files.

Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

Hello Peter, On May 23, 2013, at 4:49 AM, Peter Cock wrote: On Wed, May 22, 2013 at 9:59 PM, Greg Von Kuster g...@bx.psu.edu wrote: I cannot guarantee it, but this may be related to a fix I just committed that populates the repository tag in the dependency definitions with a toolshed

Re: [galaxy-dev] Suggestion for Latest revision: installation errors

Hello Peter, I've added the following Trello card for this: https://trello.com/card/toolshed-enhance-rss-feeds-to-include-installation-errors-related-to-automated-functional-tests/506338ce32ae458f6d15e4b3/884 On May 23, 2013, at 4:43 AM, Peter Cock wrote: On a related point, it would be

Re: [galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

On Thu, May 23, 2013 at 4:58 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, On May 23, 2013, at 4:49 AM, Peter Cock wrote: On Wed, May 22, 2013 at 9:59 PM, Greg Von Kuster g...@bx.psu.edu wrote: As an aside, the XML comment line seems not to show up properly in the HTML diff view on

[galaxy-dev] XML files for MACS v1.4

HI all, I am trying to integrate MACS v1.4 into Galaxy. But I am unable to find the XML for the following MACS tools 1) elandexport2bed 2) elandmulti2bed 3) elandresult2bed 4) macs14 5) sam2bed 6) wignorm Any pointer/guidance is appreciated. Thanks, VJ.

[galaxy-dev] Problem about main.g2.bx.psu.edu is taking too long to respond.

Dear Galaxy team, I have problem with my galaxy because I can 't check my data. I refresh my page several time but it keep report the connection has timed out. Please let me know what should I do to fix this problem. Thanks, Chureerat ___

[galaxy-dev] problem with current galaxy to submit job to drmaa/sge

Hello galaxy-dev gurus, I was trying to upgrade my galaxy server... I removed the old galaxy-dist and ran hg clone https://bitbucket.org/galaxy/galaxy-dist/ restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy. After some twiddling, I see the error