ncibtep@nih.gov

Bioinformatics Training and Education Program

BTEP Question Forum

BTEP maintains several Question and Answer Forums of interest to the NCI/CCR community.
Currently, there are forums on these topics listed below:

If you wish to ask a question go to the Ask Question Page and submit your question.

 Back to Questions

How to quickly activate bioinfo in biowulf?

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

1 Answer:

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'  

Answered on May 11th, 2020 by