Re: [galaxy-dev] galaxy and torque - resource allocation

Was hoping someone with an actual torque cluster would respond. I think the way you would configure this might be for instance might be setting native_specification like "-l nodes=1:ppn=n". Depending on how things are configured or simply because I am ignorant - this may be wrong - but I think what

Re: [galaxy-dev] dataset collections

On Wed, Jan 21, 2015 at 11:02 AM, Jorrit Boekel wrote: > Hi all, > > I’m toying around a little in galaxy-dist with the dataset collections > feature. Since I know this is work in progress, I was wondering about some > things I haven’t really found online. > > It seems to work really well to run

Re: [galaxy-dev] Setting a file download link in Galaxy help

The help text is interpreted as reStructuredText ( http://docutils.sourceforge.net/rst.html) not HTML. Here is an example link for the citation used in Galaxy's MAF tools - it demonstrates one way to create links in tools using restructuredtext: If you use this tool, please cite `Blankenberg D, T

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

On Wed, Jan 21, 2015 at 6:54 PM, John Chilton wrote: > On Wed, Jan 21, 2015 at 10:35 AM, Wolfgang Maier > wrote: >> >> >> On 21.01.2015 16:11, John Chilton wrote: >>> >>> So the tool dependency stuff didn't change - but the local job runner >>> now behaves like the other job runners (DRMAA, PBS,

Re: [galaxy-dev] Manually installing rsem_datatypes package from toolshed

I believe this is an ancient bug that I has been fixed in Galaxy's central branch but is not in the latest release: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 The previous workaround for this bug was that one would need to import the datatype at t

[galaxy-dev] Manually installing rsem_datatypes package from toolshed

I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes I see two files: 1) datatypes_conf.xml, and 2) rsem.py

[galaxy-dev] dataset collections

Hi all, I’m toying around a little in galaxy-dist with the dataset collections feature. Since I know this is work in progress, I was wondering about some things I haven’t really found online. It seems to work really well to run a tool on a list of datasets, and a new job is run for each list i

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

Hi, Could this be related to the fact that galaxy is not seeing the tools that are installed in /usr/local/bin?? I'm on latest_2015.01.13 and since the two last upgrades I saw that interproscan and bsmap were not found by galaxy. Both are installed in /usr/local and when invoked on the command

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

On 21.01.2015 16:11, John Chilton wrote: So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? This is a to

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? I need to think about how to solve this more generally bu

Re: [galaxy-dev] Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories

Just an update on that. I found out that if I put back the migrated_tool_conf.xml and shed_tool_conf.xml back in the galaxy_dist root, I can now reset metadata on most of the repositories (but not all) Same error as before pops up in paster.log for those not working. Cheers! Yves Gagnon F

Re: [galaxy-dev] Unable to get data from UCSC

Hi John, we just figured out the problem. Had to follow the instructions at https://wiki.galaxyproject.org/Admin/Config/ApacheProxy: SSL If you place Galaxy behind a proxy address that uses SSL (e.g. https:// URLs), set the following in your Apache config: Toggle line numbers

Re: [galaxy-dev] Unable to get data from UCSC

Hi John, Unfortunately swapping out this line for the one in the previous version does not work, but get this error when trying to use ucsc rather than just when transferring back: Blocked loading mixed active content " http://genome.ucsc.edu/cgi-bin/hgTables"; Also, we are serving galaxy over ht

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

Yes, this is the local job runner on a single machine. On 01/20/2015 06:52 PM, John Chilton wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wol