Advanced Parameters

There are many additional parameters that may be specified when running the primary script.

usage: [-h] [-c CHRONOS] [-m MARATHON] [-i BUILD_IMAGE]
                       [-es ENS_SPECIES] [-srcs SRC_CLASSES] [-ff] [-tm]
                       [-wd WORKING_DIR] [-cp CODE_PATH] [-sd [STORAGE_DIR]]
                       [-dp DATA_PATH] [-lp LOGS_PATH] [-ep EXPORT_PATH]
                       [-sp SRC_PATH] [-myh MYSQL_HOST] [-myp MYSQL_PORT]
                       [-myd MYSQL_DIR] [-mym MYSQL_MEM] [-myc MYSQL_CPU]
                       [-mycf MYSQL_CONF] [-myu MYSQL_USER] [-myps MYSQL_PASS]
                       [-rh REDIS_HOST] [-rp REDIS_PORT] [-rd REDIS_DIR]
                       [-rm REDIS_MEM] [-rc REDIS_CPU] [-rps REDIS_PASS]

As a developer, you may modified the src/ code and/or build your own kn_builder Docker image. To test your your development code, use a command like this:

python3 $MYCODEDIR/src/code/ \
    -i $MYIMAGE:latest \
    -cp $MYCODEDIR/src/code \
    -es drosophila_melanogaster \
    -srcs kegg,,blast

The parameters can be grouped into four different categories.

Run arguments

--chronos CHRONOS           url of chronos scheduler or LOCAL or DOCKER
--marathon MARATHON         url of marathon scheduler
--build_image BUILD_IMAGE   docker image name to use for kn_build
--ens_species ENS_SPECIES   ,, separated list of ensembl species to run
                            in setup pipeline
--src_classes SRC_CLASSES   ,, separated list of source keywords to run
                            in parse pipeline
--force_fetch               fetch even if file exists and has not
                            changed from last run
--test_mode                 run in test mode by only printing commands

Path arguments

--working_dir WORKING_DIR   absolute path to toplevel working directory
--code_path CODE_PATH       absolute path of code directory
--storage_dir [STORAGE_DIR] name of toplevel directory of storage
--data_path DATA_PATH       relative path of data directory from
--logs_path LOGS_PATH       relative path of data directory from
--export_path EXPORT_PATH   relative path of export directory from
--src_path SRC_PATH         relative path of srcClass directory from

MySQL arguments

--mysql_host MYSQL_HOST     address of mySQL db
--mysql_port MYSQL_PORT     port for mySQL db
--mysql_dir MYSQL_DIR       absolute directory for MySQL db files
--mysql_mem MYSQL_MEM       memory for deploying MySQL container
--mysql_cpu MYSQL_CPU       cpus for deploying MySQL container
--mysql_conf MYSQL_CONF     config directory for deploying MySQL
--mysql_user MYSQL_USER     user for mySQL db
--mysql_pass MYSQL_PASS     password for mySQL db

Redis arguments

--redis_host REDIS_HOST     address of Redis db
--redis_port REDIS_PORT     port for Redis db
--redis_dir REDIS_DIR       absolute directory for Redis db files
--redis_mem REDIS_MEM       memory for deploying redis container
--redis_cpu REDIS_CPU       cpus for deploying redis container
--redis_pass REDIS_PASS     password for Redis db