diff --git a/README.md b/README.md index 3e7a21b..ad36b12 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,48 @@ EVA Submission Command Line Interface for Validation ## Installation -TBD +There are currently three ways to install and run the tool: using conda, from source using Docker, +and from source natively (i.e. managing dependencies on your own). + +### Conda + +The most straightforward way to install eva-sub-cli and its dependencies is through conda. +For example the following installs eva-sub-cli in a new environment called `eva`, activates the environment, and prints +the help message: +```bash +conda create -n eva -c conda-forge -c bioconda eva-sub-cli +conda activate eva +eva-sub-cli.py --help +```` + +### From source using Docker + +This method requires just Python 3.8+ and [Docker](https://docs.docker.com/engine/install/) to be installed. +Then either clone the git repository, or download the newest tagged release from [here](https://github.com/EBIvariation/eva-sub-cli/tags): +```bash +git clone git@github.com:EBIvariation/eva-sub-cli.git +# OR +wget -O eva-sub-cli.zip https://github.com/EBIvariation/eva-sub-cli/archive/refs/tags/v0.2.zip +unzip eva-sub-cli.zip +``` + +Then install the library and its dependencies as follows (e.g. in a virtual environment): +```bash +cd eva-sub-cli +pip install -r requirements.txt +python setup.py install +``` + +### From source natively + +This method requires the following: +* Python 3.8+ +* [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) 21.10+ +* [biovalidator](https://github.com/elixir-europe/biovalidator) 2.1.0+ +* [vcf-validator](https://github.com/EBIvariation/vcf-validator) 0.9.6+ + +Install each of these and ensure they are available on the path. +Then git clone the repo or install the newest release as described above. ## Input files for the validation and submission tool @@ -46,6 +87,9 @@ More detail documentation to follow ## Execution +Note for Docker users: for each of the below commands, add the command line option `--executor docker`, which will +fetch and manage the docker container for you. + ### Validate and submit your dataset To validate and submit run the following command diff --git a/bin/eva-sub-cli.py b/bin/eva-sub-cli.py index 1008328..a4de0b5 100755 --- a/bin/eva-sub-cli.py +++ b/bin/eva-sub-cli.py @@ -55,7 +55,7 @@ def validate_command_line_arguments(args, argparser): 'previous runs. Selecting SUBMIT will run validate only if the validation was not performed ' 'successfully before and then run the submission.') argparser.add_argument('--executor', choices=[DOCKER, NATIVE], default=NATIVE, - help='Select an execution type for running validation') + help='Select an execution type for running validation (default native)') credential_group = argparser.add_argument_group('Credential', 'Specify the Webin credential you want to use to ' 'upload to the EVA') credential_group.add_argument("--username", help="Username used for connecting to the ENA webin account")