Difference between revisions of "Hail"
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Johnbullard (talk | contribs) (Created page with "Category:Software Category:Biology Category:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|Hail}} |{{#vardefine:url|https://hail.is/}} <!--CONFIGURATI...") |
Johnbullard (talk | contribs) m (Make log and temp example paths more generic) |
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$ python | $ python | ||
>>> import hail as hl | >>> import hail as hl | ||
| − | >>> '''hl.init(log='/ | + | >>> '''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 = hl.balding_nichols_model(n_populations=3,n_samples=10,n_variants=100) | ||
>>> mt.show() | >>> mt.show() | ||
Latest revision as of 17:42, 19 October 2021
Description
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.
System Variables
- HPC_HAIL_DIR - installation directory
- HPC_HAIL_BIN - executable directory
Additional 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). An example of this initialization in an interactive Python session is in bold below:
$ 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()