c-sar

| Master | Develop | | --------------------------------------------- | ----------------------------------------------- | | | |

• Notes
  • CRISPRcleanR v1.2.1
• Developer notes
  • Version numbers
  • Submodules
  • Changing branches
  • Editing the submodule
  • Updating the submodule
  • pre-commit
  • Updating licence headers
• LICENSE

Notes

CRISPRcleanR v1.2.1

The version of CRISPRcleanR in the GitHub DESCRIPTION does not match the latest release version 1.2.1 which is defined in build/installRpackages.sh.

Developer notes

Version numbers

The version is in 2 files, please ensure it is updated on each release:

• Dockerfile
• nextflow.config

Submodules

This project has a submodule to make it easier to build the docker image. The initial checkout needs to be done via recursive strategy:

```bash

new checkout

git clone --recurse-submodules git@....git

existing checkout

cd repo

update local metadata (new branches etc)

git fetch

check branch, switch if necessary

git status

pull any changes

git pull

populate the submodule

git submodule update --init --recursive ```

Changing branches

If you change branches you need to make sure the submodule changes with you:

bash git checkout --recurse-submodules $NEW_BRANCH

Editing the submodule

You can edit a submodule directly in this checkout and commit back to the original repository, however it is generally less confusing to consider the submodule as a read-only component. If you want to push changes made in this way please see the official git documentation linked above.

Updating the submodule

Generally submodules are only updated to specific commits and tags. To change which commit your branch refers to:

```bash cd submodules/rcrispr git pull git checkout ${TAGORCOMMITREF} cd ../../ git status

you will see the submodule is listed as dirty

git commit -m "Updated RCRISPR submodule to ${TAGORCOMMITREF}" submodules/rcrispr ```

pre-commit

Please install a pre-commit to your user environment (not a venv):

```bash curl https://pre-commit.com/install-local.py | python3 -

may need to add to PATH

in repo folder, enable pre-commit hooks

pre-commit install ```

Updating licence headers

Please use skywalking-eyes.

Expected workflow:

```bash

recent build, change to apache/skywalking-eyes:0.2.0 once released

export DOCKER_IMG=ghcr.io/apache/skywalking-eyes/license-eye ```

1. Check state before modifying .licenserc.yaml:
   • docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header check
   • You should get some 'valid' here, those without a header as 'invalid'
2. Modify .licenserc.yaml
3. Apply the changes:
   • docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header fix
4. Add/commit changes

The check is executed in the CI pipeline which will fail if expected files are missing the license.

DO NOT edit the header in the files, please modify the date component of content in .licenserc.yaml. The only files needing manual update being:

• README.Rmd

If you need to make more extensive changes to the license carefully test the pattern is functional.

LICENSE

``` Copyright (c) 2021 Genome Research Ltd

Author: CASM/Cancer IT cgphelp@sanger.ac.uk

This file is part of C-SAR.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’. ```