A simple shell script to automate the process of downloading EuPathDB resources of interest for a given set of organisms.
To use, place the script in the base directory where you plan to download resources to.
Edit fetch_latest.sh to include the databases and organisms you wish to
retrieve, and run to download all corresponding resources.
Currently the script automates the downloading of:
- Genome FASTA
- Annotated Proteins FASTA
- Annotated CDSs FASTA
- Genome GFF
- Genome annotation TXT
- Codon usage TXT
- Gene aliases TXT
Large files such as the genome annoation TXT are gzipped, and bowtie2 indices are built for each genome FASTA file.