[galaxy-dev] htseq-count/deseq2 conda dependency issues

Dear devs I've recently encountered some strange issues when running the htseq-count and deseq2 tools installed from the toolshed onto our production instance. In both cases there have been problems with a couple of the conda dependency installations. Specifically: - For htseq-count, runs

[galaxy-dev] Monitoring Dashboard for Galaxy

I remember there previously being an additional tool that ran on a different port from galaxy that allowed for monitoring of performance and jobs running. Is this tool still packaged with galaxy and if so how can it be activated. ___

Re: [galaxy-dev] Monitoring Dashboard for Galaxy

Hi Evan I assume you are talking about the 'reports' tool? Have a look here: https://galaxyproject.org/admin/usage-reports/ https://docs.galaxyproject.org/en/latest/admin/reports.html Additional (system) information about each executed job can be logged by activating plugins in the

[galaxy-dev] Galaxy Conda resolver install Issue

I just ran across an issue when attempting to load galaxy. I am not sure how to fix this issue or what could be causing it. Conda is installed properly. File "/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 58, in paste_app_factory app =

Re: [galaxy-dev] Job output not returned from Cluster Error

Presuming SGE runs this on a remote node, it's likely the file hasn't been flushed to disk. Have you checked to see if the files eventually show up? Sent from my iPhone > On 17. Aug 2017, at 17:49, Yip, Miu ki wrote: > > Hi, > > We’re having a bit of an error where the GUI

[galaxy-dev] Job output not returned from Cluster Error

Hi, We’re having a bit of an error where the GUI shows that a job had an error. When the user submits the job, the job is seen to have run via terminal and uge. The job working directory exists and the out and error file is in there. Once the job completes, it seems like the GUI will say that

Re: [galaxy-dev] htseq-count/deseq2 conda dependency issues

Hi Peter, indeed the defaults channel should now be the lowest priority of all conda channels. This recommended setting in galaxy.ini is now conda_ensure_channels = iuc,bioconda,conda-forge,defaults,r Unfortunately these changes appear as changes are made within bioconda, which usually do not

Re: [galaxy-dev] Galaxy Conda resolver install Issue

Hello Evan, this looks suspiciously like a bug that Matthias Bernt has fixed on the development branch a while back. I have backported this to Galaxy release 17.01 and release 17.05. If you update your galaxy branch to the latest commit it should work (or you should receive a more instructive