Updating the configuration file¶
- Edit the ELASPIC configuration file ./config/config_file.ini to match your system:
- Settings in the [SEQUENCE] section should be modified to match the location of your local BLAST and PDB databases.
- Settings in the [DATABASE] section should be modified to match the local MySQL, PostgreSQL, or SQLite database.
- Settings in the [DEFAULT] and [MODEL] may be left unchanged, since the default values are good enough in most cases.
Configuration options¶
[DEFAULT]¶
- global_temp_dir
- Location for storing temporary files. It will be used only if the
TMPDIR
environmental variable is not set. Default = ‘/tmp/’. - temp_dir string
- A folder in the global_temp_dir that will contain all the files that are relevant to ELASPIC. Inside this folder, every job will create its own unique subfolder. Default = ‘elaspic/’.
- debug
- Whether or not to show detailed debugging information. If True, the logging level will be set to
logging.DEBUG
. If False, the logging level will be set tologging.INFO
. Default = True. - look_for_interactions
- Whether or not to compute models of protein-protein interactions. Default = True.
- remake_provean_supset
- Whether or not to remake the Provean supporting set if one or more sequences cannot be found in the BLAST database. Default = False.
- n_cores
- Number of cores to use by programs that support multithreading. Default = 1.
- web_server
- Whether or not the ELASPIC pipeline is being run as part of a webserver. Default = False.
- provean_temp_dir
- Location to store provean temporary files if working on any note other than beagle or banting. For internal use only. Default = ‘’.
- copy_data
- Whether or not to copy calculated data back to the archive. Set to ‘False’ if you are planning to copy the data yourself (e.g. from inside a PBS or SGE script). Default = True.
[SEQUENCE]¶
- blast_db_dir
- Location of the blast nr and pdbaa databases.
- blast_db_dir_fallback
- Place to look for blast nr and pdbaa databases if blast_db_dir does not exist.
- matrix_type
- Substitution matrix for calculating the mutation conservation score. Default = ‘blosum80’.
- gap_start
- Penalty for starting a gap when calculating the mutation conservation score. Default = -16.
- gap_extend
- Penalty for extending a gap when calculating the mutation conservation score. Default = -4.
[MODEL]¶
- modeller_runs
- Number of models that MODELLER should make before choosing the best one. Not implemented! Default = 1.
- foldx_water
-CRYSTAL
: use water molecules in the crystal structure to bridge two protein atoms.-PREDICT
: predict water molecules that make 2 or more hydrogen bonds to the protein.-COMPARE
: compare predicted water bridges with bridges observed in the crystal structure.-IGNORE
: don’t predict water molecules. Default.
Source: http://foldx.crg.es/manual3.jsp.
- foldx_num_of_runs
- Number of times that FoldX should evaluate a given mutation. Default = 1.
[DATABASE]¶
- db_type
- The database that you are using. Supported databases are MySQL, PostgreSQL, and SQLite.
- sqlite_db_dir
- Location of the SQLite database. Required only if db_type is SQLite.
- db_schema
- The name of the schema that holds all elaspic data.
- db_schema_uniprot
- The name of the database schema that holds uniprot sequences. Defaults to db_schema.
- db_database
- The name of the database that contains db_schema and db_schema_uniprot. Required only if db_type is PostgreSQL. Defaults to db_schema.
- db_username
- The username for the database. Required only if db_type is MySQL or PostgreSQL.
- db_password
- The password for the database. Required only if db_type is MySQL or PostgreSQL.
- db_url
- The IP address of the database. Required only if db_type is MySQL or PostgreSQL.
- db_port
- The listening port of the database. Required only if db_type is MySQL or PostgreSQL.
- db_socket
- Path to the socket file, if it is not in the default location.
Used only if db_url is localhost.
For example:
/usr/local/mysql5/mysqld.sock
for MySQL and/var/lib/postgresql
for PostgreSQL. - schema_version
- Database schema to use for storing and retreiving data. Default = ‘elaspic’.
- archive_type
- extracted: all archive files are contained in an extracted directory tree.
- 7zip: archive is made of three compressed 7zip files (provean/provean.7z, uniprot_domain/uniprot_domain.7z, uniprot_domain_pair/uniprot_domain_pair.7z), provided on the elaspic downloads page.
- archive_dir
- Location for storing and retrieving precalculated data.
- pdb_dir
- Location of all pdb structures, equivalent to the “data/data/structures/divided/pdb/” folder in the PDB ftp site. Optional.