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ALTA\n\n Reliable foundation library to access infrastructure elements for next generation sequencing data analysis and management \n \n## Requirements:\n\n- Python 2.7\n- [OMERO.biobank](https://github.com/crs4/omero.biobank)\n- [BioBlend](https://github.com/galaxyproject/bioblend)\n- [nglimsclient](https://bitbucket.org/crs4/nglimsclient)\n- [python-irodsclient](https://github.com/irods/python-irodsclient)\n- [bikaclient](https://github.com/ratzeni/bika.client)\n- [vcfminerclient](https://github.com/ratzeni/vcf-miner.client)\n- [comoda](https://github.com/gmauro/comoda)\n\n\n\n## Installation\n\n\n```bash\ncurl -sS http://gmauro.github.io/alta/install.sh | sh -s venv\n```\nIn your current path, you will find a virtual enviroment into the 'venv' dir.  \nActivate it to access Alta.\n```bash\nsource venv/bin/activate\n```\n\n## Usage\n\n\n### Connect to a Bika server:\n```python\nfrom alta.bims import Bims\nbk = Bims('http://host', 'user', 'password', 'bikalims')\n```\nthen to access [bikaclient](https://github.com/ratzeni/bika.client) methods, use\n```python\nbk.bims.client\n\u003cbikaclient.BikaClient instance at 0x7f94b1a26e60\u003e\n```\ninstead to access alta.bims methods, use:\n```python\nbk.bims\n\u003calta.bims.bikalims.BikaLims at 0x7ff03c68c4d0\u003e\n```\n\n### Connect to an iRODS server\n```python\nfrom alta.objectstore import build_object_store\nir = build_object_store(store='irods', host=host, user=user, password=password, zone=zone)\n```\nthen to access alta.objectore.yrods methods, use:\n```python\nir\n\u003calta.objectstore.yrods.IrodsObjectStore object at 0x7f050742c990\u003e\n```\n\n### Connect to a VCFMiner server\n```python\nfrom alta.browsers import Browsers\nmc = Browsers('http://host', 'user', 'password', 'vcfminer')\n```\nthen to access [vcfminerclient](https://github.com/ratzeni/vcf-miner.client) methods, use\n```python\nmc.browsers.client\n\u003cvcfminerclient.VCFMinerClient instance at 0x7f94b1a26e60\u003e\ninstead to access alta.bims methods, use:\n```python\nbk.bims\n\u003calta.bims.bikalims.BikaLims at 0x7ff03c68c4d0\u003e\n``````\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmauro%2Falta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgmauro%2Falta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmauro%2Falta/lists"}