Hail

Description

hail website

Hail is an open-source Python library that simplifies genomic data analysis. It provides powerful, easy-to-use data science tools that can be used to interrogate even biobank-scale genomic data (e.g. UK Biobank, gnomAD, TopMed, FinnGen, and Biobank Japan).

Environment Modules

Run module spider hail to find out what environment modules are available for this application.

Environment Variables

• HPC_HAIL_DIR - installation directory
• HPC_HAIL_BIN - executable directory

Additional Usage Information

The Hail session object must be initialized with a log file to which you have write access (the default instance will try to write logs to the application directory, which will fail). Here is an example of this initialization in an interactive Python session:

$ module load hail/0.2.77
$ python
>>> import hail as hl
>>> hl.init(log='/blue/groupname/username/hail/test.log', tmp_dir='/blue/groupname/username/hail/tmp')
>>> mt = hl.balding_nichols_model(n_populations=3,n_samples=10,n_variants=100)
>>> mt.show()

Categories

biology, genomics