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https://github.com/bcgsc/pori_cbioportal
cBioportal adaptor for creating PORI reports in IPR
https://github.com/bcgsc/pori_cbioportal
genomics personalized-medicine pori
Last synced: 7 days ago
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cBioportal adaptor for creating PORI reports in IPR
- Host: GitHub
- URL: https://github.com/bcgsc/pori_cbioportal
- Owner: bcgsc
- License: gpl-3.0
- Created: 2020-12-18T01:13:29.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2022-01-22T13:03:38.000Z (almost 3 years ago)
- Last Synced: 2023-08-19T06:10:26.496Z (about 1 year ago)
- Topics: genomics, personalized-medicine, pori
- Language: Python
- Homepage: https://bcgsc.github.io/pori
- Size: 47.9 KB
- Stars: 2
- Watchers: 6
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PORI cBioportal
 [](https://pypi.org/project/pori_cbioportal) [](https://doi.org/10.5281/zenodo.5730701)
This repository is part of the [Platform for Oncogenomic Reporting and Interpretation (PORI)](https://bcgsc.github.io/pori).
This python package uses the IPR and GraphKB PORI adaptors to create PORI reports from dumps
of cbioportal data.
## Getting Started
### Install via pip
```bash
pip install pori_cbioportal
```
### Download Study Data
Study data should be downloaded from cbioportal, for example
```bash
wget https://cbioportal-datahub.s3.amazonaws.com/laml_tcga_pan_can_atlas_2018.tar.gz
tar -xvzf laml_tcga_pan_can_atlas_2018.tar.gz
```
The folder should have the variant and metadata files, for example
```text
laml_tcga_pan_can_atlas_2018
|-- data_clinical_patient.txt
|-- data_clinical_sample.txt
|-- data_CNA.txt
|-- data_fusions.txt
|-- data_log2CNA.txt
|-- data_mutations_extended.txt
`-- data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt
```
### Generate Reports
This is then used to generate individual reports for all patients included in the study.
Note to do this you will need access to both a GraphKB server for matching and an IPR
server for upload.
```bash
pori_cbioportal laml_tcga_pan_can_atlas_2018 \
--study_id "LAML TCGA" \
--password $PASSWORD \
--ipr_url https://YOUR_IPR_API_HOST/api \
--graphkb_url https://YOUR_GRAPHKB_API_HOST/api
```
The loader will expect default names for the files but this can be overwritten with the other command line arguments. See the help menu for more options
```bash
pori_cbioportal --help
```
## Getting Started (For developers)
### Install
clone this repository
```bash
git clone ssh://[email protected]:7999/dat/pori_cbioportal.git
cd pori_cbioportal
```
create a virtual environment
```bash
python3 -m venv venv
source venv/bin/activate
```
install the package and its development dependencies
```bash
pip install -e .[dev]
```
Run the tests
```bash
pytest tests
```
### Deployment (Publishing)
Install the deployment dependencies
```bash
pip install .[deploy]
```
Build the distribution files
```bash
python setup.py install sdist bdist_wheel
```
Upload the distibutions to the package server (-r defined in your pypirc)
```bash
twine upload -r bcgsc dist/*
```
### Deployment (Scripts)
A buildout config is included by default which will build all console scripts defined
in the package.
create a virtual environment and install buildout
```bash
python3 -m venv venv
source venv/bin/activate
pip install -U pip setuptools zc.buildout
```
run buildout
```bash
buildout
```
This will create a directory `bin` with the executable scripts