https://github.com/gmauro/alta
Reliable foundation library to access infrastructure elements for next generation sequencing data analysis and management
https://github.com/gmauro/alta
python python-library
Last synced: 3 months ago
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Reliable foundation library to access infrastructure elements for next generation sequencing data analysis and management
- Host: GitHub
- URL: https://github.com/gmauro/alta
- Owner: gmauro
- Created: 2015-04-27T09:55:38.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2018-03-16T14:39:22.000Z (over 7 years ago)
- Last Synced: 2025-02-03T11:14:30.144Z (5 months ago)
- Topics: python, python-library
- Language: Python
- Homepage:
- Size: 64.5 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# ALTA
Reliable foundation library to access infrastructure elements for next generation sequencing data analysis and management
## Requirements:
- Python 2.7
- [OMERO.biobank](https://github.com/crs4/omero.biobank)
- [BioBlend](https://github.com/galaxyproject/bioblend)
- [nglimsclient](https://bitbucket.org/crs4/nglimsclient)
- [python-irodsclient](https://github.com/irods/python-irodsclient)
- [bikaclient](https://github.com/ratzeni/bika.client)
- [vcfminerclient](https://github.com/ratzeni/vcf-miner.client)
- [comoda](https://github.com/gmauro/comoda)
## Installation
```bash
curl -sS http://gmauro.github.io/alta/install.sh | sh -s venv
```
In your current path, you will find a virtual enviroment into the 'venv' dir.
Activate it to access Alta.
```bash
source venv/bin/activate
```
## Usage
### Connect to a Bika server:
```python
from alta.bims import Bims
bk = Bims('http://host', 'user', 'password', 'bikalims')
```
then to access [bikaclient](https://github.com/ratzeni/bika.client) methods, use
```python
bk.bims.client
```
instead to access alta.bims methods, use:
```python
bk.bims
```
### Connect to an iRODS server
```python
from alta.objectstore import build_object_store
ir = build_object_store(store='irods', host=host, user=user, password=password, zone=zone)
```
then to access alta.objectore.yrods methods, use:
```python
ir
```
### Connect to a VCFMiner server
```python
from alta.browsers import Browsers
mc = Browsers('http://host', 'user', 'password', 'vcfminer')
```
then to access [vcfminerclient](https://github.com/ratzeni/vcf-miner.client) methods, use
```python
mc.browsers.client
instead to access alta.bims methods, use:
```python
bk.bims
``````