ALTA

Reliable foundation library to access infrastructure elements for next generation sequencing data analysis and management

Requirements:

• Python 2.7
• OMERO.biobank
• BioBlend
• nglimsclient
• python-irodsclient
• bikaclient
• vcfminerclient
• comoda

Installation

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.

source venv/bin/activate

Usage

Connect to a Bika server:

from alta.bims import Bims
bk = Bims('http://host', 'user', 'password', 'bikalims')

then to access bikaclient methods, use

bk.bims.client
<bikaclient.BikaClient instance at 0x7f94b1a26e60>

instead to access alta.bims methods, use:

bk.bims
<alta.bims.bikalims.BikaLims at 0x7ff03c68c4d0>

Connect to an iRODS server

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:

ir
<alta.objectstore.yrods.IrodsObjectStore object at 0x7f050742c990>

Connect to a VCFMiner server

from alta.browsers import Browsers
mc = Browsers('http://host', 'user', 'password', 'vcfminer')

then to access vcfminerclient methods, use

mc.browsers.client
<vcfminerclient.VCFMinerClient instance at 0x7f94b1a26e60>
instead to access alta.bims methods, use:
```python
bk.bims
<alta.bims.bikalims.BikaLims at 0x7ff03c68c4d0>