View source for Hail

[[Category:Software]]
[[Category:Biology]]
[[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|Hail}}
|{{#vardefine:url|https://hail.is/}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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).


<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==

{{Note|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:|info}}

 $ 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()
 
|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

WRITE_CITATION_HERE

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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