GVA2023 Day 1 Environment Checkup and Catchup

Owned by Deatherage, Daniel E
Last updated: Jun 18, 2023
2 min read

Overview

This is mostly for anyone who didn't attend Monday's class for whatever reason. While the setup tutorial is full of useful information, this turns that tutorial into a black box and accomplishes the requirements needed for other tutorials to work. It is highly recommended that you at least read through the entire setup tutorial when you have time.

Objectives

  1. Verify course bashrc file is active
  2. Verify conda is installed

Logging in with ssh

If you need help logging into stampede2 the powershell and terminal tutorials are available if you need help remembering how to do this.

.bashrc

After logging in, You should see the following prompt:

tacc:~$

If you do it means you successfully have copied and activated the .bashrc file which controls a number of variables.

ONLY if you see something else should you use the commands in this section


Use mv to change your .profile file to a backup copy
cdh
mv .profile profile_pre_GVA_backup
mv .bashrc bashrc_pre_GVA_backup
cp /corral-repl/utexas/BioITeam/gva_course/GVA.bashrc .bashrc
cp /corral-repl/utexas/BioITeam/gva_course/GVA.profile .profile
chmod 700 .bashrc
chmod 700 .profile
logout

after logging back in with ssh you should see the following:

tacc:~$

If not, get my attention.

conda

Activate a conda environment
conda activate base

If your prompt now changes to:

(base) tacc:~$

It means you have successfully installed miniconda and should skip the following warning block.

ONLY if you see something different should you use the commands in this section


Using the mkdir command to create a folder named 'src' inside of your $WORK directory
cd $WORK
mkdir src
cd src
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Following the installation prompts you will need to:

  1. hit enter to page through the license agreement
  2. enter 'yes' to agree to said license agreement
  3. enter to confirm the default installation location

  4. enter 'yes'  to initialize Miniconda3 by running conda init?


As per the directions at the end of the installation process, logout, log back in, and disable conda base environment being activated.
logout
#log back in using the ssh command. 
conda config --set auto_activate_base false
conda config --set channel_priority strict
logout
log back in a final time
conda activate base

if the above worked correctly, your prompt should go from 

tacc:~$

to 

(base) tacc:~$

If you see anything else, get my attention.


You can now continue directly to the Read Mapping Tutorial or launch an idev session. 

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