Software requirements

• Basic Linux programs (pip or apt-get, git, Python 3)
• Python dependencies: numpy, scipy, matplotlib, openpyxl, requests, biopython
• APRICOT software from PyPI: bio-apricot
• Latest CDD database: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
• Latest InterPro databases and InterProScan: ftp://ftp.ebi.ac.uk/pub/databases/interpro
• InterProScan requires pfsearch wrapper and Java 8 or above
• BLAST executables (from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (psiblast, rpsblast, blastp, makeblastdb)
• Gene Ontology (go.obo)
• PDB files: proteins sequence and secondary-structure and PDB to InterPro mapping
• Taxonomy data
• needle from EMBOSS software
• Psortb for localization prediction (only for the subcomand addanno)
• RaptorX for secondary structure presiction (only for the subcomand addanno)

Click here, to see the explanation of the database requirement and their structure.

Please see the instructions for working with the Docker image.

In case, users do not wish to run Docker image, the complete file system with the tool and dataset can be installed using the shell script APRICOT/shell_scripts/apricot_minimum_required_files.sh. Please see the instructions for local installation.