Adds environment.yml file that will create a conda environment named escapevariants with all the required conda packages. Removes module loading from individual scripts that now use the conda environment.
Adds a new installation step to the README to create the conda environment:
Changes use of picard to use picard instead of java due to challenges finding the location of the picard.jar file within a
conda environment.
The setup-escape-variants.sh script now must be run using sbatch or interactive session.
Fixes #36
Changes to requirements
Some requirements required minor version updates to work with the conda environment.
picard-tools/2.4.1-gcb01 was upgraded to picard=2.25.0
perl/5.10.1-fasrc04 was upgraded to perl=5.32.0
Note
To avoid running out space in your home directory on HARDAC when creating the conda environment you may want to set the envs_dirs in your conda config file. Add something similar to the the following to your .condarc file:
Adds environment.yml file that will create a conda environment named
escapevariantswith all the required conda packages. Removes module loading from individual scripts that now use the conda environment.Adds a new installation step to the README to create the conda environment:
More details are in the README.
Changes use of picard to use
picardinstead ofjavadue to challenges finding the location of the picard.jar file within a conda environment.The setup-escape-variants.sh script now must be run using sbatch or interactive session.
Fixes #36
Changes to requirements
Some requirements required minor version updates to work with the conda environment.
Note
To avoid running out space in your home directory on HARDAC when creating the conda environment you may want to set the
envs_dirsin your conda config file. Add something similar to the the following to your .condarc file: