add script to setup CSD3 accounts

utils/setup_csd3.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# see https://github.com/cambiotraining/hpc-intro/issues/46
+
+# backup bashrc
+cp ~/.bashrc ~/.bashrc_bkp
+
+# unzip data to hpc-work
+unzip ~/rds/rds-introhpc/data.zip -d ~/rds/hpc-work/hpc_workshop
+
+# install mamba
+bash ~/rds/rds-introhpc/Miniforge3-$(uname)-$(uname -m).sh -b -p $HOME/miniforge3
+$HOME/miniforge3/bin/mamba init
+source ~/.bashrc
+conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge
+conda config --set remote_read_timeout_secs 1000
+
+# set R up
+mamba install -y -n base r-argparse==2.2.2
+
+# additional conda environments
+mamba create -y -n scipy scipy==1.12.0 numpy==1.26.4 matplotlib==3.8.3
+mamba create -y -n mapping bowtie2==2.5.3