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Merged
skiggety merged 4 commits into from
Nov 19, 2019
Merged

readme changes for SCP-1905 #50

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readme changes for SCP-1905
skiggety Nov 14, 2019
afa31e8
Allowing for non-broad employees
skiggety Nov 14, 2019
fc29bf9
delete stray comment
skiggety Nov 14, 2019
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Merge branch 'master' into sl-git-secrets
skiggety Nov 18, 2019
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30 changes: 18 additions & 12 deletions README.md
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Expand Up @@ -4,7 +4,7 @@ File Ingest Pipeline for Single Cell Portal
[![Build status](https://img.shields.io/circleci/build/github/broadinstitute/scp-ingest-pipeline.svg)](https://circleci.com/gh/broadinstitute/scp-ingest-pipeline)
[![Code coverage](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline/branch/master/graph/badge.svg)](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline)

The SCP Ingest Pipeline is an ETL pipeline for single-cell RNA-seq data.
The SCP Ingest Pipeline is an ETL pipeline for single-cell RNA-seq data.

# Prerequisites
* Python 3.6+
Expand Down Expand Up @@ -41,24 +41,30 @@ vault read secret/kdux/scp/development/$BROAD_USER/mongo/hostname
export DATABASE_HOST="<ip from Vault (omit brackets)>"
```

## Git hooks
After installing Ingest Pipeline, add Git hooks to help ensure code quality:
```
pre-commit install && pre-commit install -t pre-push
```
The hooks will expect that [git-secrets](https://github.com/awslabs/git-secrets) has been set up. If you are a Broad Institute employee who has not done this yet, please see: [broadinstitute/single_cell_portal_configs](https://github.com/broadinstitute/single_cell_portal_configs) for specific guidance.

### Bypass hooks
In rare cases, you might need to skip Git hooks, like so:

* Skip commit hooks: `git commit ... --no-verify`
* Skip pre-push hooks: `git push ... --no-verify`

# Test
After installing:
```
source env/bin/activate
cd tests; pytest
```

# Use
See [`ingest_pipeline.py`](https://github.com/broadinstitute/scp-ingest-pipeline/blob/ew-tests-hook/ingest/ingest_pipeline.py) for usage examples.

# Git hooks
After installing Ingest Pipeline, add Git hooks to help ensure code quality:
Run this every time you start a new terminal to work on this project:
```
pre-commit install && pre-commit install -t pre-push
source env/bin/activate
```

## Bypass hooks
In rare cases, you might need to skip Git hooks, like so:

* Skip commit hooks: `git commit ... --no-verify`

* Skip pre-push hooks: `git push ... --no-verify`
See [`ingest_pipeline.py`](https://github.com/broadinstitute/scp-ingest-pipeline/blob/ew-tests-hook/ingest/ingest_pipeline.py) for usage examples.