diff --git a/LICENSE b/LICENSE index 816b682..370b8f6 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2020-2021, Manuel Holtgrewe +Copyright (c) 2020-2023, Berlin Institute of Health, Manuel Holtgrewe Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 558f2e7..63fac2f 100644 --- a/README.md +++ b/README.md @@ -4,39 +4,35 @@ # VarFish CLI -Command line interface for [VarFishServer](https://github.com/bihealth/varfish-server). +Command line interface for [bihealth/varfish-server](https://github.com/bihealth/varfish-server). -## Getting Started +> [!NOTE] +> This repository focuses on the command line interface program `varfish-cli`. +> If you are new to VarFish, you may want to start at the repository [bihealth/varfish-server](https://github.com/bihealth/varfish-server). -- [VarFish Homepage](https://www.cubi.bihealth.org/software/varfish/) -- [Manual](https://varfish-server.readthedocs.io/en/latest/) - - [Installation Instructions](https://varfish-server.readthedocs.io/en/latest/admin_install.html) -- [Docker Compose Installer](https://github.com/bihealth/varfish-docker-compose#run-varfish-server-using-docker-compose) +## Installation -## VarFish Repositories +You can install `varfish-cli` from [bioconda](https://bioconda.github.io/): -- [varfish-server](https://github.com/bihealth/varfish-server) -- - The VarFish Server is the web frontend used by the end users / data analysts. -- [varfish-annotator](https://github.com/bihealth/varfish-annotator) -- - The VarFish Annotator is a command line utility used for annotating VCF files and converting them to files that can be imported into VarFish Server. -- [varfish-cli](https://github.com/bihealth/varfish-cli) -- - The VarFish Command Line Interface allows to import data through the VarFish REST API. -- [varfish-db-downloader](https://github.com/bihealth/varfish-db-downloader) -- - The VarFish DB Downloader is a command line tool for downloading the background database. -- [varfish-docker-compose](https://github.com/bihealth/varfish-docker-compose) -- - Quickly get started running a VarFish server by using Docker Compose. - We provide a prebuilt data set with some already imported data. +To create a new conda environment named `varfish-cli` with the package: -## Installation +``` +mamba create -y -n varfish-cli -c bioconda varfish-cli +conda activate varfish-cli +varfish-cli --help +``` -### From Source +To get help with individual sub commands: + +``` +varfish-cli importer +# OR +varfish-cli importer --help +``` -```bash -$ git clone git@github.com:bihealth/varfish-cli.git -$ cd varfish-cli -$ conda create -n varfish-cli python=3.7 -$ conda activate varfish-cli -$ pip install -e . +You will also need to create a configuration file in your home folder with the server address: + +``` $ cat >~/.varfishrc.toml <=3.10 + +Clone the repository: + +``` +git clone git@github.com:bihealth/varfish-cli.git +cd varfish-cli-ng +``` + +Now, create a virtualenv and install the software and its development requirements: +``` +virtualenv venv +source venv/bin/activate + +pip install -r requirements/develop.txt +pip install -e . +``` -`varfish-cli` is also available as a pip-Package. -Preferably install into a separate venv. +Finally, create the configuration file: -```bash -$ pip install varfish-cli +``` $ cat >~/.varfishrc.toml < + +cd utils/terraform +terraform init +terraform import github_repository.varfish-cli varfish-cli +terraform validate +terraform fmt +terraform plan +terraform apply +``` diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..c3402f9 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,27 @@ +# For more configuration details: +# https://docs.codecov.io/docs/codecov-yaml + +# Check if this file is valid by running in bash: +# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate + +# Coverage configuration +# ---------------------- +coverage: + status: + patch: false + + range: 70..80 # First number represents red, and second represents green + # (default is 70..100) + round: down # up, down, or nearest + precision: 2 # Number of decimal places, between 0 and 5 + +# Ignoring Paths +# -------------- +# which folders/files to ignore + +# Pull request comments: +# ---------------------- +# Diff is the Coverage Diff of the pull request. +# Files are the files impacted by the pull request +comment: + layout: diff, files # accepted in any order: reach, diff, flags, and/or files diff --git a/utils/terraform/.gitignore b/utils/terraform/.gitignore new file mode 100644 index 0000000..5dfe310 --- /dev/null +++ b/utils/terraform/.gitignore @@ -0,0 +1,2 @@ +.terraform* +terraform.tfstate* diff --git a/utils/terraform/main.tf b/utils/terraform/main.tf new file mode 100644 index 0000000..2034098 --- /dev/null +++ b/utils/terraform/main.tf @@ -0,0 +1,30 @@ +# Mangement of the GitHub project. + +resource "github_repository" "varfish-cli" { + name = "varfish-cli" + description = "VarFish REST API client (CLI + Python package)" + homepage_url = "https://github.com/bihealth/varfish-cli" + visibility = "public" + topics = [ + "bioinformatics", + "genetics", + "varfish", + "vcf", + ] + + has_issues = true + has_downloads = true + has_discussions = false + has_projects = false + + allow_auto_merge = true + allow_rebase_merge = false + allow_merge_commit = false + + delete_branch_on_merge = true + + vulnerability_alerts = true + + squash_merge_commit_message = "BLANK" + squash_merge_commit_title = "PR_TITLE" +} diff --git a/utils/terraform/provider.tf b/utils/terraform/provider.tf new file mode 100644 index 0000000..2dc05b1 --- /dev/null +++ b/utils/terraform/provider.tf @@ -0,0 +1,9 @@ +terraform { + required_providers { + github = { + source = "integrations/github" + } + } +} + +provider "github" {}