Admin kit

The screen program

screen is a useful linux program that creates, attach, detach or reattach "virtual" shell sessions. screen allows to run simultaneous linux processes in isolated environments which can be put in the background while working with the console at other tasks

A handful of screen commands you should know:

  • screen -ls lists all screen sessions available, attached (currently active) or detached in the background
  • screen -r <session> reattaches a detached screen session.
  • within an active screen session CtrlA then D detaches the active session
  • within an active screen session type exit to terminate the active session
  • screen -S <session> creates a new session
  • screen -d -r <session> detaches the current session and reattach another one

See the Galaxy server logs

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

tail -f ./galaxy/database/gravity/log/gunicorn.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
after activating the proper conda environment

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 /root/galaxy/database/dependencies/_conda/bin/activate
Then 
conda clean --all