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mz_generic_params.md

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Parameters for mz_genenic runner

The process flow is controlled by setting few variables. The most accurate and uptodate list of them is in the conf/_mz.conf file.

There are few ways to specify these parameters.

  • By using shell environment variables
  • By placing (and editing) _mz.conf to the directory mz_generic.sh is run from,
  • By specifying/setting a single shell variable MZ_CONFIG=<path_to_conf_file> with the patch to config file

Environmental parameters (variables)

Parameter Example Description Comment
MZ_CONFIG /path/to/_mz.conf Paths to the config files with the listed below options, sourced by mz_generic.sh
MZ_RELEASE 51 EnsemblGenomes release version
ENS_VERSION 104 Ensembl (core db schema) release version
CMD cmd_server_alias SQL DB server alias, to create core DB at and put e-hive DBs for running pipelines
PROD_SERVER prod_server_alias Production SQL DB server alias to get ensembl_production and ncbi_taxonomy databases from Should be exported within config file (export PROD_SERVER)

Usage and commnad line arguments

First parameter -- [meta configuration file](../(docs/metaconf.md)

For most of the use cases the meta configuration file (meta-file) should be provide as the first option:

./ensembl-production-metazoa/scripts/mz_generic.sh ${METACONF_DIR}/<meta_conf_file>

You can use either:

  • abs-path
  • or relative to the dir you're running scripts fromi
  • or just name of the meta configuration file to be searched for in ./ensembl-production-metazoa/meta/${ENS_VERSION} dir

I.e.

./ensembl-production-metazoa/scripts/mz_generic.sh ./ensembl-production-metazoa/meta/109_for_110/dmel

Though, you can use "help" and "env_setup_only" (see below) options instead of meta-file path on their own

./ensembl-production-metazoa/scripts/mz_generic.sh help

Second (optional) parameter

In addition to the meta conf paramete you can provide additional option, that controls the generic loader scripts/mz_generic.sh behaviour:

Option Description Comments
help print usage and exit
env_setup_only prepare environment and exit
restore [tag_pattern] restore from the latest back up, or from the one matching "tag_pattern" move bup symlink, if you need something older than the last saved; when pattern is used, back-ups that followed the macthing are removed (drops everything fresher then the one it's restoring from). N.B. as many ${DATA_DIR}/<meta_name>/done tags as you need (use ls -lt to sort tags by time).
stop_after_conf get data, validate, prepare cofiguration for the loader and stop
stop_after_load stop after the loader pipeline before running anything else
stop_before_xref stop before running xref helper
pre_final_dc run datachecks before patching to the new schema stage active, only if the goal is reachable
finalise create back up with the final tag active, only if the goal is reachable
patch_schema patch schema to the latest available

Ad-hoc environment setup

Sometimes there's a need to have Ensembl environment, that can be used by unrelated pipelines / workflows.

To setup environment

configs_dir=$(pwd)
cd $configs_dir

git clone [email protected]:Ensembl/ensembl-production-metazoa.git

# source ensembl-production-metazoa/conf/_mz.conf file
# or 
export PROD_SERVER=<prod_server_alias>

export ENS_VERSION=107

# setup environment (you should have proper github keys/permissions in place)
./ensembl-production-metazoa/scripts/mz_generic.sh env_setup_only 2>&1 | tee env_setup.log

cd ${configs_dir}
ln -s ensembl.prod.${ENS_VERSION} ensembl.prod

# source environment settings
source ${configs_dir}/ensembl.prod.${ENS_VERSION}/setup.sh