galaxyproject/cloudman

17.09 release todo

afgane opened this issue · 1 comments

afgane commented

17.09 will still be a minor-update release with the following being known issues from earlier releases to be fixed then:

  • Update IE images being staged
  • Include /mnt/galaxy/galaxy-app/config/plugins/interactive_environments/jupyter/config/jupyter.ini to set use_volumes = False (unless error when loading a BAM file is resolved docker: Error response from daemon: Invalid bind mount spec "/mnt/galaxy/files/000/dataset_9.dat:/import/[9] MergeSamFiles on data 7, data 6, and data 5: Merged BAM dataset.bam:rw": Invalid volume specification: '/mnt/galaxy/files/000/dataset_9.dat:/import/[9] MergeSamFiles on data 7, data 6, and data 5: Merged BAM dataset.bam:rw'.)
  • Set command_inject = -e DEFAULT_CONTAINER_RUNTIME=900 in jupyter.ini
  • Include /mnt/galaxy/galaxy-app/config/plugins/interactive_environments/rstudio/config/rstudio.ini and set use_volumes = False
  • Update galaxy.ini proxy settings as per https://docs.galaxyproject.org/en/master/admin/interactive_environments.html#configuring-the-proxy
  • Update nginx's conf (galaxy.locations) to fix the incorrect url prefix for IEs (it includes /galaxy/...)
  • Update conda_channels in galaxy.ini to iuc,bioconda,conda-forge,defaults,r
nuwang commented

Closing because old version.