ADMIN TOOL KIT

All commands below should be run as the admin user (sudo -i)

see your slurm jobs triggered by Galaxy

watch "squeue --format '%.18i %.9P %.40j %.8u %.2t %.10M %.4C %.6D %R' && sinfo"

If your slurm cluster is stuck (the datasets stay in the "grey state" forever)

  • the previous command should show it
  • then try this:
scontrol update NodeName=<name of your instance> State=Resume

See the Galaxy server logs

When some tools are failing, you may grab useful information. 

tail -f /home/galaxy/galaxy/uwsgi.log

If tools fail with libssl / openssh issue in the bug report

cd /lib/x86_64-linux-gnu
ln -s libssl.so.1.1 libssl.so.1.0.0
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0
We are not fan of this, it is a rather dirty turnaround

For Conda Geek only

In case of problems with some conda packages, you may try command like: 

conda install -c bioconda samtools=1.9 --force-reinstall
conda install -c bioconda --force-reinstall ucsc-genepredtobed ucsc-gtftogenepred

To shrink you _conda dependencies folder

This folder is located at /home/galaxy/tool_dependencies/_conda and you must first activate the Galaxy conda base environment using the command (from anywhere): 

source /home/galaxy/tool_dependencies/_conda/bin/activate
Then 
conda clean --dry-run --all

In case of many issues with many tools

There is a problem with your conda tool dependencies.

You can use the 💫 magic patch 💫

Copy and paste the code below in the (root) terminal. This will swap your _conda environment with a clean, fresh one.

cd ~ && \
wget https://raw.githubusercontent.com/ARTbio/Run-Galaxy/master/deployment_scripts/patch_conda_env.sh && \
sh patch_conda_env.sh