Configuration Files and Data Directories

• /home/camoco/.camoco

This is the storage directory for all camoco related data. This can be kept in the container, but it will not be persistent then. It is highly recommended to mount a directory for this.

• /home/camoco/cob.conf

This is the location of the cob configuration file that is used by cob by default. This will not work by default given no data is included in this docker image. Make sure to build your configuration based off your data and mount it here.

• /home/camoco/.camoco.conf

This is the location of the camoco configuration file. By default the emable camoco config file in this repo is used. This should work fine for most use cases.

Configuration

A powerful configuration engine is provided to both set options for the server and also options for the content for the website, such as default option values. As mentioned above, these can either be provided through a standalone YAML configuration file example.conf is included in the repo) or in a section with the same format titled web in the main camoco configuration file (found at ~/.camoco.conf). One need not include one at all, this will just be started with the default values (seen below). This will also trigger all available Camoco networks and GWAS datasets to be loaded in. To prevent this, one may specify the desired datasets. The following is an annotated version of the default settings, showing all the potential configuration options:

Server Options

name: cob          # The name of this server instance, must be unique for
                   # each instance, can be overridden by '-n' flag
port:    50000     # Port to which the server will be attached
host:    localhost # The allowed hosts that can communicate with this server
                   # (must be 0.0.0.0 with docker or to allow external connections)
threads: 8         # How many individual threads the sever process may use
timeout: 500       # How long a thread maybe unresponsive before termination
dev:     False     # Forces JS and CSS to be recompiled on every request
                   # Normally done only on server restart

Datasets

networks:            # Camoco networks that are to be loaded in the server.
    - My_Network_1   # If this is not included, all available Camoco
    - My_Network_2   # networks will be loaded.
gwas:                # GWAS datasets that will be loaded in the server. If
    - My_GWAS_1      # this is not included, all GWAS datasets that
                     # correspond to loaded networks will be loaded.

Default Values

defaults:         # This is the dictionary containing all of the defaults
                  # for the options on the web site
logSpacing: True  # Spacing of genes in Polywas layout, log or true distance
visEnrich: True   # Only enrich genes visible on graph or all in table
fdrFilter: True   # Whether to use FDR to filter query results
nodeCutoff: 1     # How many edges a node must have to be visible
edgeCutoff: 3.0   # The cutoff for significance of edge scores
fdrCutoff: 0.35   # If the FDR Filter is used, the cutoff for being visible
windowSize: 50000 # Window size used in the query
flankLimit: 2     # Flank limit used in the query
visNeighbors: 25  # Default number of neighbors visible in custom network
nodeSize: 10      # Size of the nodes on the graph
pCutoff: 0.05     # P value cutoff for enrichment queries
minTerm: 5        # Minimum number of genes a GO term must have to be included
maxTerm: 300      # Maximum number of genes a GO term must have to be included

Reference Links

This section allows for linking directly from genes to an external website for more information. This can be configured for each different reference genome (RefGen) used to build the included networks. If not included, the option won’t appear. To configure this,start by writing the name of the RefGen under the refLinks option, followed by a colon and a space as seen below. Then you must go to the database you wish to use for that RefGen, and search any gene. After finding this, copy the URL onto the line after the name of the RefGen. Finally replace the name of the gene in the URL with the string {id}. This allows the website to find where in the URL the gene name goes, and replace it with any gene for that organism. The following example works for maize, soybean, and medicago. Add or subtract species at will.

refLinks:
    Zm5bFGS: http://www.maizegdb.org/gene_center/gene/{id}
    Gmax_a2_V1: https://www.soybase.org/sbt/search/search_results.php?category=FeatureName&version=Glyma2.0&search_term={id}
    Mt_4.0: http://medicago.jcvi.org/cgi-bin/medicago/manatee/shared/ORF_infopage.cgi?db=mta4&user=access&password=access&identifier=locus&orf={id}