-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Browse files
Browse the repository at this point in the history
- Loading branch information
1 parent
fb15c1a
commit 0e48240
Showing
4 changed files
with
123 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
11 changes: 11 additions & 0 deletions
11
lapis2-docs/src/content/docs/maintainer-docs/references/preprocessing.mdx
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,11 @@ | ||
--- | ||
title: Preprocessing | ||
description: Reference on the SILO preprocessing | ||
--- | ||
|
||
TODO #565 | ||
|
||
- preprocessing config. Has defaults set in Docker. Only set what you need, leave the rest to the defaults | ||
- input format of data | ||
|
||
## Preprocessing config |
97 changes: 97 additions & 0 deletions
97
...s2-docs/src/content/docs/maintainer-docs/references/starting-silo-and-lapis.mdx
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,97 @@ | ||
--- | ||
title: Starting SILO and LAPIS | ||
description: Reference on how to start the SILO and LAPIS applications | ||
--- | ||
|
||
:::note | ||
The [corresponding tutorial](/maintainer-docs/tutorials/start-lapis-and-silo) | ||
shows an example step by step. | ||
This page aims to provide a full reference. | ||
::: | ||
|
||
## Starting SILO | ||
|
||
SILO can be started in two modes: | ||
|
||
- `preprocessing`: Starts the SILO preprocessing that prepares the data for the SILO API server. | ||
- `api`: Starts the SILO API server that responds to SILO queries. | ||
|
||
We provide Docker images for SILO with the name: `ghcr.io/genspectrum/lapis-silo`. | ||
Those images can be used to start SILO in both modes. | ||
|
||
### Starting the SILO preprocessing | ||
|
||
To start the SILO preprocessing you need to provide the argument `--preprocessing`. | ||
SILO will then start reading the input data, process it | ||
and terminate after the result is written to the output directory. | ||
|
||
Optionally, you can specify: | ||
|
||
- `--preprocessingConfig`: | ||
The path to the [preprocessing config](/maintainer-docs/references/preprocessing#preprocessing-config) file that SILO should use, | ||
e.g. `~/LAPIS/preprocessing_config.yaml` | ||
- `--databaseConfig`: | ||
The path to the [database config](/maintainer-docs/references/database-configuration) file that SILO should use, | ||
e.g. `~/LAPIS/database_config.yaml`. | ||
|
||
If those parameters are not provided, SILO will try to read the files from its current working directory. | ||
|
||
#### Starting the SILO preprocessing with Docker | ||
|
||
You only have to pass the argument `--preprocessing` to the Docker container. | ||
The image is constructed with defaults in a way that you only need to mount the data to the correct locations: | ||
|
||
- the preprocessing config to `/app/preprocessing_config.yaml`, | ||
- the database config to `/app/database_config.yaml`, | ||
- the data to `/preprocessing/input`, | ||
- the output directory to `/preprocessing/output`. | ||
|
||
### Starting the SILO API | ||
|
||
To start the SILO API server you need to provide the argument `--api`. | ||
It will start a web server that listens to port 8081. | ||
|
||
The SILO API will read data from a directory that can be specified (in descending order of prevalence) via: | ||
|
||
- a program argument `--dataDirectory`, | ||
- YAML file `./runtime_config.yaml` (in SILO's working directory) with the key `dataDirectory`, | ||
- the default value `./output/` (in SILO's working directory). | ||
|
||
The database config does not need to be provided. | ||
It is contained in the compiled output of the preprocessing. | ||
|
||
#### Starting the SILO API with Docker | ||
|
||
You only have to pass the argument `--api` to the Docker container. | ||
The image is constructed with a runtime config file that sets the data directory to `/data`, | ||
i.e. you only need to mount the result of the preprocessing to `/data`. | ||
|
||
## Starting LAPIS | ||
|
||
To start LAPIS you need to provide the following parameters: | ||
|
||
- `--silo.url`: The URL where SILO is running, e.g. `http://localhost:8081`. | ||
- `--lapis.databaseConfig.path`: | ||
The path to the [database config](/maintainer-docs/references/database-configuration) file that LAPIS should use, | ||
e.g. `~/LAPIS/database_config.yaml`. | ||
- `--referenceGenomeFilename`: | ||
The path to the [reference genomes](/maintainer-docs/references/reference-genomes) file that LAPIS should use, | ||
e.g. `~/reference_genomes.json`. | ||
This can alternatively be passed via the environment variable `REFERENCE_GENOME_ENV_VARIABLE_NAME`. | ||
The parameter takes precedence over the environment variable. | ||
|
||
LAPIS listens to port 8080. | ||
|
||
#### Starting LAPIS with Docker | ||
|
||
We provide Docker images for LAPIS with the name: `ghcr.io/genspectrum/lapis-v2`. | ||
|
||
The provided Docker images already contain reasonable default values for | ||
|
||
- the `lapis.databaseConfig.path` parameter: `/workspace/database_config.yaml`, | ||
- the `REFERENCE_GENOME_ENV_VARIABLE_NAME` environment variable: `/workspace/reference_genomes.json`. | ||
|
||
:::note | ||
You simply need to mount the config files to those locations in the container | ||
and start the container with `--silo.url=<your SILO URL>`. | ||
::: |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters