QuestionsCategory: BIOSTARHow to quickly activate bioinfo in biowulf?
yangz13@nih.gov asked 5 months ago

I have installed the bioinfo package in my own data directory. Right now, every time when I open a new terminal window, I have to enter the two commands below

[user@biowulf temp]$ source /data/$USER/conda/etc/profile.d/conda.sh
[user@biowulf temp]$ conda activate bioinfo

I tried both creating a bioinfo.sh shell script and defining an alias called bioinfo to
quickly activate bioinfo, but all failed. Could you please help me with that? Thanks
1 Answers
tillodc@nih.gov Staff answered 5 months ago

To bypass having to run the “source /data/$USER/conda/etc/profile.d/conda.sh” step on biowulf, you can add the following to your ~/.bash_profile :
if [ -f /data/$USER/conda/etc/profile.d/conda.sh ]; then
    . /data/$USER/conda/etc/profile.d/conda.sh
fi
 
You can then restart your biowulf session (i.e. exit then login again).  Then all you need to do to activate the bioinfo environment is type:

conda activate bioinfo

If you wish, you can alias the “conda activate bioinfo” step by adding the following to your ~/.bashrc:
alias bioinfo=’conda activate bioinfo’