Difference between revisions of "CGATools"

Latest revision as of 13:26, 15 August 2022

Description

The Complete Genomics Analysis Tools (cgatools) is an open source project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities, but a C++ API is available as well. The general areas of functionality include genome comparison, format conversion, and reference tools.

Environment Modules

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

System Variables

HPC_CGATOOLS_DIR - installation directory
HPC_CGATOOLS_BIN - executable directory

Citation

If you publish research that uses cgatools you have to cite it as follows: R. Drmanac, et. al. Science 327(5961), 78. [DOI: 10.1126/science.1181498]

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|cgatools}}
 |{{#vardefine:url|http://cgatools.sourceforge.net/}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:intel|}} <!-- "11.1" -->
-|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4" -->
-|{{#vardefine:mod|1}} <!--MODULES -->
 |{{#vardefine:exe|}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
@@ Line 25: / Line 22: @@
 <!--VERSIONS-->
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_CGATOOLS_BIN - executable directory
-* HPC_CGATOOLS_INC - includes directory
-* HPC_CGATOOLS_DOC - documentation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==