Difference between revisions of "CGATools"

Revision as of 18:01, 10 August 2012

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.

Required Modules

modules documentation

Serial

cgatools

System Variables

HPC_{{#uppercase:cgatools}}_DIR - installation directory
HPC_CGATOOLS_BIN - executable directory
HPC_CGATOOLS_INC - includes directory
HPC_CGATOOLS_DOC - documentation 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 4: / Line 4: @@
 |{{#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 29: / Line 26: @@
 ===Serial===
 *{{#var:app}}
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
+* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 * HPC_CGATOOLS_BIN - executable directory
 * HPC_CGATOOLS_INC - includes directory
 * HPC_CGATOOLS_DOC - documentation directory
-==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==
 DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY|}}