4.3. Change running options for existing tool in ProkEvo - npavlovikj/ProkEvo GitHub Wiki

In order to demonstrate how to change options for existing tool in ProkEvo, we will use MLST as an example. MLST supports different schemes, depending on the bacterial organism used. For every used tool, there is a Bash script in the directory scripts/ with the specific options used for that tool. In these scripts, the program is executed as suggested in its manual.

The available Bash script for MLST is called "mlst.sh" and looks like:

[centos@npavlovikj-prokevo ProkEvo]$ cat scripts/mlst.sh 
#!/bin/bash

source /opt/conda/etc/profile.d/conda.sh
conda activate /home/centos/ProkEvo/prokevo

# mlst "$@"
# Change scheme based on organism
mlst --legacy --scheme senterica --csv "$@"

conda deactivate

Since ProkEvo was initially developed with Salmonella in mind, the default used MLST scheme is senterica (--scheme senterica). Depending on the organism used, this scheme can be easily changed by opening and modifying the "mlst.sh" script. For example, if S. aureus is used, the MLST Bash script looks like:

[centos@npavlovikj-prokevo ProkEvo]$ vim scripts/mlst.sh 
#!/bin/bash

source /opt/conda/etc/profile.d/conda.sh
conda activate /home/centos/ProkEvo/prokevo

# mlst "$@"
# Change scheme based on organism
mlst --legacy --scheme saureus --csv "$@"

conda deactivate

Another example of program which options may need to be changed is Roary. The available Bash script for Roary is called "roary.sh" and looks like:

[centos@npavlovikj-prokevo ProkEvo]$ cat scripts/roary.sh 
#!/bin/bash

source /opt/conda/etc/profile.d/conda.sh
conda activate /home/centos/ProkEvo/prokevo

# roary "$@"
roary -s -e --mafft -p 4 -cd 99.0 -i 95 -f "$@"
tar -czvf roary_output.tar.gz roary_output

conda deactivate

While one of the many features of Roary is to produce core gene alignment, this step is time consuming and it may need to be turned off sometimes when core gene alignment is not necessary. This can be done by removing the -e --mafft option from the Roary command. For example, the modified script for Roary that excludes the core gene alignment looks like:

[centos@npavlovikj-prokevo ProkEvo]$ cat scripts/roary.sh 
#!/bin/bash

source /opt/conda/etc/profile.d/conda.sh
conda activate /home/centos/ProkEvo/prokevo

# roary "$@"
roary -s -p 4 -cd 99.0 -i 95 -f "$@"
tar -czvf roary_output.tar.gz roary_output

conda deactivate

In a similar manner, the options and thresholds of the other scripts used in ProkEvo can be modified.