Configuration¶

MPACT is configured with environment variables. Every one is optional and has a working default. With Docker, set them under environment: in docker-compose.yml or in an env_file.

Storage and limits¶

Variable	Default	Purpose
`MPACT_DATA_ROOT`	`server/var`	Workspaces, uploads and run outputs
`MPACT_MAX_CONCURRENT_JOBS`	`2`	Analyses running at once; more are queued
`MPACT_JOB_TIMEOUT_SECONDS`	`3600`	Time limit per analysis
`MPACT_MAX_UPLOAD_BYTES`	`536870912`	Largest upload (512 MB)
`MPACT_SESSION_MAX_AGE_SECONDS`	`2592000`	Workspaces untouched this long (30 days) are deleted, at startup and daily

Each analysis is its own process, and a large peak table can use several GB of memory. Allow one concurrent job per 2 cores and 4 GB.

Reference data¶

Variable	Default	Purpose
`MPACT_REFERENCE_DIR`	`server/data`	Directory for the files below
`MPACT_NPATLAS_PATH`	`<reference>/npatlas.tsv`	Natural Products Atlas table
`MPACT_NPATLAS_SUPPLEMENTAL_PATH`	`server/data/npatlas_supplemental.tsv`	Extra compounds searched with NPAtlas (SIDERITE siderophores, a lab compound list)
`MPACT_TAXONOMY_PATH`	`server/data/npatlas_taxonomy.tsv`	Genus lineages for the taxon filter
`MPACT_SIDERITE_KEYS_PATH`	`server/data/siderite_inchikeys.txt`	Structures for the siderophore filter
`MPACT_MSMS_LIBRARY_PATH`	`<reference>/msdial_msms.npz`	Compiled MS/MS library
`MPACT_MSMS_META_PATH`	`<reference>/msdial_msms_meta.tsv.gz`	MS/MS library names and structures

Performance¶

Variable	Default	Purpose
`MPACT_MAX_HEATMAP_ROWS`	`1500`	Rows drawn in the heatmap; beyond this, neighbouring rows are averaged
`MPACT_PVCLUST_NBOOT`	`1000`	Bootstrap iterations for dendrogram support values
`MPACT_CSV_CACHE_MB`	`256`	Memory for parsed output tables
`MPACT_PLOT_CACHE_MB`	`64`	Memory for finished plots, so reopening a tab is instant
`MPACT_FRAGDB_CACHE_ENTRIES`	`6`	Parsed fragment databases kept in memory
`MPACT_PREWARM`	`true`	Parse NPAtlas structures at startup so the first substructure search is fast

Security and networking¶

Variable	Default	Purpose
`MPACT_AUTH`	`none`	Sign-in mode: `none`, `code`, `users` or `email`. See Sign-in and accounts
`MPACT_SECRET_KEY`	generated	Key that signs login cookies; generated into the data root if unset
`MPACT_AUTH_MAX_AGE_SECONDS`	`1209600`	How long a sign-in lasts (14 days)
`MPACT_SESSION_COOKIE_SECURE`	`false`	Send cookies over HTTPS only; turn on behind TLS
`MPACT_TRUST_PROXY`	`false`	Read the client address from `X-Forwarded-For`; only behind your own proxy
`MPACT_DEV`	`false`	Include exception details in API errors; never in production

Variables for each sign-in mode, including email delivery, are listed on Sign-in and accounts.

Demo datasets¶

Demo datasets live in server/data/demo/. A dataset whose files are missing is left out of the list. Delete the directory to hide the demo panel completely.