[galaxy-dev] Installing Galaxy, Conda and Python

Hola, We are attempting to install Galaxy, from git, version 17.05 We largely have it installed, but seem to be falling over at the installation of dependencies. In particular, conda via Galaxy can't find Gnuplot 4.6, and the conda libraries don't show a gnuplot < 5.x The error: 10.126.160.84

[galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

Hi, Does anyone know if a data manager exists in the tool shed for creating and integrating NCBI BLAST+ indices within galaxy? I can't seem to find it in the tools shed or searching the internet Surly such a tool must exist. Any info would be greatly appreciated. Thanks, David David Kovalic

[galaxy-dev] Galaxy Project @ Johns Hopkins is hiring

Hello all, The Galaxy Project at Johns Hopkins is hiring software engineers and postdocs: The Taylor Lab at Johns Hopkins University in Baltimore, Maryland is hiring software engineers and post-docs to work

Re: [galaxy-dev] openms python3 & print

Hi Matthias, we have encountered similar issues on our instance and we solved it (with help of Björn Grüning) differently: we have added python in the requirements-tag of the corresponding xml file. Assuming that you use conda for dependency resolution, this could help. HTH, Eugen > On

Re: [galaxy-dev] numpy problem

On Tue, Aug 8, 2017 at 8:01 AM, Matthias Bernt wrote: > Dear dev-list, > > here an answer to my own question. > > The problem was that the tool "Group data by a column and perform aggregate > operation on other columns." returned an error: > > Traceback (most recent call last):

Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

There is an open issue for these paths not working with vanilla Galaxy tools https://github.com/galaxyproject/galaxy/issues/1676. -John On Wed, Aug 9, 2017 at 10:03 AM, Peter Cock wrote: > I'm puzzled now too, cross reference > >

Re: [galaxy-dev] openms python3 & print

Hi Nicola and Bjoern, thanks a lot for the informations. I'm just installing the suite. Best, Matthias On 10.08.2017 16:08, Nicola Soranzo wrote: Hi Matthias, I think you're using an old version of the tool, the one at

Re: [galaxy-dev] openms python3 & print

Hi Matthias, please note that this repo is 4 years old. We have changed the wrappers quite a bit in the last years and now you have it here: suite_openms Or every tool has its own repo. Last update yesterday. Hope that helps, Bjoern P.S. I have deprecated the old repo. On 10.08.2017 15:03,

Re: [galaxy-dev] openms python3 & print

Hi Matthias, I think you're using an old version of the tool, the one at https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_decoydatabase/178e00cf12d7 doesn't use a Python wrapper. The development repository is at https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms

[galaxy-dev] openms again

Hi, just fixed the print() issue locally and ran into the next problems which were easy to fix: - ConfigParser -> configparser - iteritems -> items (The modified sources are attached if they are of interest) Now I have an error that seems to be deeper: Failed to find specific OpenMS option

[galaxy-dev] openms python3 & print

Hi, I got an error from OpenMS which seems to be related to python3: Fatal error: Exit code 1 (Error running OpenMS tool.) File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py", line 22 print "Running shell