Commit c5c12dab authored by José Mª. Fernández's avatar José Mª. Fernández
Browse files

Added script to build containers. Also, docker tag being used should depend on...

Added script to build containers. Also, docker tag being used should depend on the repository, not on latest
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Showing with 28 additions and 4 deletions
+28 -4
#!/bin/sh
set -e
scriptdir="$(dirname "$0")"
case "${scriptdir}" in
/*)
true
;;
.)
scriptdir="$(pwd)"
;;
*)
scriptdir="$(pwd)/${scriptdir}"
;;
esac
DOCKER_TAG="${1:-latest}"
docker build -t "transbionet_cnv:${DOCKER_TAG}" "${scriptdir}/container"
......@@ -14,7 +14,7 @@ The workflow takes an input file with CNV predictions (i.e. the results provided
## Usage
In order to use the workflow you need to:
* Install [Nextflow](https://www.nextflow.io/)
* Clone this in a separate directory, and build locally the Docker image found in [the 'container' folder](../container). Use the following command ```docker build -t transbionet_cnv:latest .```.
* Clone this in a separate directory, and build locally the Docker image found in [the 'container' folder](../container). If you are in the same directory as this README, use the following command ```../build-containers.sh 20220826```.
* Run it just using *`nextflow run main.nf`*. Arguments specifications:
```
Usage:
......
......@@ -30,3 +30,7 @@ Some notes and considerations:
In case of any doubt, please, contact by email to Pablo Minguez and Lorena de la Fuente, chairs of the task, together with the INB Hub.
Have a look at the [**Relevant Literature References**](./RelevantLiterature.md) for further information on the articles cited here.
# Workflow execution details
The details are available at [1stChallenge/nextflow/README.md](1stChallenge/nextflow/README.md).
......@@ -10,18 +10,18 @@ profiles {
docker {
process {
withName: validation{
container = "transbionet_cnv:latest"
container = "transbionet_cnv:20220826"
}
}
process {
withName: compute_metrics{
container = "transbionet_cnv:latest"
container = "transbionet_cnv:20220826"
}
}
process {
withName: benchmark_consolidation{
container = "transbionet_cnv:latest"
container = "transbionet_cnv:20220826"
}
}
......
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