dockerization.md

Install and Configure Lifemapper on Docker

Containers

• Backend (PostgreSQL server)
• Compute
• NGinx (PostgreSQL client)
• System test (lmtest and specify-openapi-tools)
• Solr
• Flask

Environment variables

• from [lifemapper-server] (https://github.com/lifemapper/lifemapper-server/blob/main/src/version.mk)
• from [lifemapper-compute] (https://github.com/lifemapper/lifemapper-compute/blob/main/src/version.mk)

System dependencies

Flask container only:

• mapserver 7.0.0 (including mapserver-bin, libmapserver2, python3-mapscript)
• webclient (lifemapper/viz-client repo)
• mod-wsgi ?
• lmdata-image [lifemapper-server] (https://github.com/lifemapper/lifemapper-server/blob/main/src/lmdata-image/prepData.sh.in) scripts and Environment variables above to pull data
• geotiff (package manager)

Solr container only:

• solr (docker hub?)

Backend container only:

• PostgreSQL 9.6 (docker hub)
• Postgis2
• psycopg2-binary (python pip install)
• lmdata-species [lifemapper-server] (https://github.com/lifemapper/lifemapper-server/blob/main/src/lmdata-species/prepData.sh.in) scripts and Environment variables above to pull data

Backend and Compute containers:

• lmdata-env [lifemapper-server] (https://github.com/lifemapper/lifemapper-server/blob/main/src/lmdata-env/prepData.sh.in) scripts and Environment variables above to pull data. Put data in shared volume;
• [lmpy] (https://github.com/lifemapper/lmpy)
• [biotaphypy] (https://github.com/biotaphy/BiotaPhyPy)
• requests
• scipy (includes numpy)
• matplotlib
• idigbio
• dendropy
• gdal (not from pip, use package manager)
  • libgdal26, libgdal-dev, python3-gdal

Testing container:

• [lmtest] (https://github.com/lifemapper/lmtest/)
• specify-open-api-tools (specify/open_api_tools repo)

Source or binary installs

• [cctools] (http://ccl.cse.nd.edu/software/downloadfiles.php)

Installation resources

Combine Environmental variables and values with

• variables in lifemapper/core/LmServer/config/config.lmserver.ini and values in lifemapper-server/src/version.mk
• variables in lifemapper/core/LmCompute/config/config.lmcompute.ini and values in lifemapper-compute/src/version.mk

Process

• XML files with [Backend post-install instructions] (https://github.com/lifemapper/lifemapper-server/tree/main/nodes) for directory and user setup

• [Backend Post-install and config script] (https://github.com/lifemapper/lifemapper-server/blob/main/src/rocks-lifemapper/initLM.in)

• XML files with [Compute post-install instructions] (https://github.com/lifemapper/lifemapper-compute/tree/main/nodes) for directory and user setup

• [Compute Post-install and config script] (https://github.com/lifemapper/lifemapper-compute/blob/main/src/rocks-lmcompute/initLMcompute.in)

Misc

Move helper shell scripts from roll repos lifemapper-server/src/rocks-lifemapper and lifemapper-compute/src/rocks-lmcompute into core/bin