Re: [galaxy-dev] init scripts version 16.01

Hi Marius, Now I ran in to some problems. When trying to change metadata of a file, the python path changes (these tools run using drmaa) to the normal system version. Here tools are ending in error becaus sqlalchemy.orm cannot be found. I can ofcourse install sqlarchemy-python systemwide. But th

Re: [galaxy-dev] init scripts version 16.01

Hi Eric, Take a look at this https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#wheel-interaction-with-other-software . I hope that should be sufficient. Cheers, Marius On 11 April 2016 at 14:25, Eric Kuyt wrote: > Hi Marius, > > Now I ran in to some problems. > > When

Re: [galaxy-dev] init scripts version 16.01

We had something similar breaking when using run-as-real-user, where config/galaxy.ini setting external_chown_script which defaults to scripts/external_chown_script.py was being run on the cluster nodes using the system default Python. Here we created a wrapper shell script which invoked the Pytho

[galaxy-dev] About Local Galaxy Tool Problem

Hi, I want to convert .bcl file (data from illumina NextSeq500) to fastq. Firstly, i tried Galaxy on public server and it became success. But i have large dataset and i couldnt wait for weeks to solve. Then, i set up Galaxy locally. But most of tools dissappared in menu. I tried to upload publ

Re: [galaxy-dev] Galaxy Bare/Core and custom upload tool

Hi Björn, > Yes it is, but you need the :dev version, DOH, I should have known… > Can you explain what you delete? I do really support this idea as we are > also developing cheminformatics or imaging flavours. Currently I think I have just removed the datatypes. I haven’t removed anything els

Re: [galaxy-dev] Galaxy Bare/Core and custom upload tool

[Resending because GMail keeps mangling my email address…] Hi Björn, > Yes it is, but you need the :dev version, DOH, I should have known… > Can you explain what you delete? I do really support this idea as we are > also developing cheminformatics or imaging flavours. Currently I think I have

[galaxy-dev] IUC Hackathon - Conda dependencies

Hi! On monday 04/04, @bgruening and some members of Galaxy team (me and @nitesh1989 at least) would want to get a Hackathon on adding IUC / Devteam tools Conda dependencies. Hackathon begins at: 2pm (UTC-4) / 8pm (UTC+2). It will be

Re: [galaxy-dev] Galaxy Bare/Core and custom upload tool

[Resending (again) as GMail keeps mangling my email address… sorry for triple posting...] Hi Björn, > Yes it is, but you need the :dev version, DOH, I should have known… > Can you explain what you delete? I do really support this idea as we are > also developing cheminformatics or imaging flav

[galaxy-dev] Data manager problem

Hello, I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and und

Re: [galaxy-dev] Planemo test with SGE

Did you ever figure this out? I cannot think of anything that would cause this - if the job conf is working with Galaxy it should work with planemo. Are you sure Galaxy was actually using the configuration and not just the local runner. Is it possible you've modified run.sh to modify the environme

Re: [galaxy-dev] Planemo test with SGE

Hi John, No I haven't been able to figure this out. In answer to your questions, I haven't modified the run.sh. I do however specify that "upload1" tool be run on destination "local" since cluster nodes are configured such that they can't communicate with the outside world which would prevent some