https://github.com/deib-geco/docker_viruclust
https://github.com/deib-geco/docker_viruclust
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/deib-geco/docker_viruclust
- Owner: DEIB-GECO
- License: apache-2.0
- Created: 2021-12-17T15:41:01.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-02-11T15:56:41.000Z (over 3 years ago)
- Last Synced: 2025-06-04T22:11:49.619Z (4 months ago)
- Size: 17.6 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Docker ViruClust
Prerequisites:
- the user must have installed Docker Desktop (https://www.docker.com/products/docker-desktop)
- the user must have a .tsv file with sequences' metadata from GISAID. This can be retrieved, e.g., by logging to https://www.gisaid.org/ and downloading the 'metadata' file from Download packages menu. Here follows the expected header with one example line:
| Virus name | Type | Accession ID | Collection date | Location | Additional location information | Sequence length | Host | Patient age | Gender | Clade | Pango lineage | Pangolin version | Variant | AA Substitutions | Submission date | Is reference? | Is complete? | Is high coverage? | Is low coverage? | N-Content | GC-Content
| --- | --- | --- | --- |--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
hCoV-19/Italy/XXX/2020 | betacoronavirus | EPI_ISL_XXXXXX | 2020-01-01 | Europe / Italy / Italy | | 29903 | Human | unknown | unknown | G | B.1 | 2021-01-01 | | (NSP15_A283V,NSP12_P323L,Spike_D614G) | 2020-04-17 | | True | True | | 0.0068649119282 | 0.379674275888 |
How to start ViruClust:
1) Download the `docker-compose.yml` file.
2) Open terminal.
3) In terminal, go to the directory of the `docker-compose.yml` file.
4) Run the command: `FILE_PATH=/path_of_directory_of_tsv FILE_NAME=name.tsv docker-compose up`, where:
- FILE_PATH is the path of the directory that contains the .tsv previously downloaded from GISAID.
- FILE_NAME is the name of the .tsv file.
5) Wait until the process finishes to insert all the data in the database (big .tsv files ~5GB could require a few hours).
6) When the log on the terminal shows the message `* Running on http://0.0.0.0:5000/ (Press CTRL+C to quit)`, the database has been loaded and the application can be opened in a browser using the following URL: http://localhost:5000/viruclust/.
The process can be stopped with CTRL+C; it can be restarted using the same or a new .tsv file, requiring to rerun the whole upload.
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**A WIKI of the tool is available at https://github.com/DEIB-GECO/ViruClust/wiki**