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Updating the configuration file

Edit the ELASPIC configuration file ./config/config_file.ini to match your system:
  1. Settings in the [SEQUENCE] section should be modified to match the location of your local BLAST and PDB databases.
  2. Settings in the [DATABASE] section should be modified to match the local MySQL, PostgreSQL, or SQLite database.
  3. 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 to logging.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.

Environmental variables

PATH

A colon-separated list of paths where ELASPIC should look for required programs, such as BLAST, T-coffee, Modeller, and cd-hit.

TMPDIR

Location to store all temporary files and folders.