Docker #25

bkmarzouk · 2023-11-23T10:28:19Z

Docker build for soprano. Some changes in repo structure to accommodate easier build data mounts.

ensembl_downloads is the primary location for downloads from the ensembl ftp server sitting in the root of the rep. Subfolders here, .e.g homo_sapiens, can be mounted quite straigtforwardly on server side. Moreover, downloaded data files won't be copied from src on docker build if users run this after locally using the repo.
Commands like docker run -d -p 8501:8501 --name hub_soprano -e SOPRANO_DISABLE_DOWNLOADS=True icrsc/soprano:latest can spin up the container. SOPRANO_DISABLE_DOWNLOADS=True prevents users from downloading reference files. Should mount data to /app/ensembl_downloads/homo_sapiens.

…ner is running

…nts)

…ce size. (<3Gb now)

bkmarzouk added 14 commits November 21, 2023 10:27

update ignore for new ensembl cache def

30605b5

relocate chrom and fai files to new location

a230634

update path defs to point to new ensembl cache location

b9c1c4a

App runs via container: http://localhost:8501/ to access after contai…

9a6c0d3

…ner is running

redundent vcf files for previous experimentation

dad1da7

enable option to disable genome downloads (useful for server deployme…

da0fe3c

…nts)

Updates to order of layer caching & tidying up of image a bit to redu…

354d2b7

…ce size. (<3Gb now)

Decompress transcript IDs in docker build

342a508

test build and push

de937ec

syntax ./Dockerfile -> Dockerfile

79afb4c

omit context and file args

7ac715e

update tags to match repo

1e4181c

[skip-ci] notes in docker file

0e61a42

[skip ci] update branch in docker workflow to point to main only

8515433

bkmarzouk merged commit c2e6a7d into python-dev Nov 23, 2023

bkmarzouk deleted the docker branch November 23, 2023 10:28

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