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 13: / Line 10: @@
 |{{#vardefine:testing|}} <!--TESTING/PROFILING-->
 |{{#vardefine:faq|}} <!--FAQ-->
-|{{#vardefine:citation|}} <!--CITATION-->
+|{{#vardefine:citation|1}} <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 19: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 <!--VERSIONS-->
-==Available versions==
+<!--Modules-->
-* 1.5.0.31
+==Environment Modules==
-<!-- -->
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-{{#if: {{#var: mod}}|==Running the application using modules==
+==System Variables==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 * HPC_CGATOOLS_BIN - executable directory
-* HPC_CGATOOLS_INC - includes directory
-* HPC_CGATOOLS_DOC - documentation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==
@@ Line 43: / Line 38: @@
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 <!--Policy-->
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 <!--Performance-->