SOAPdenovo-Trans: Difference between revisions

Revision as of 19:52, 10 August 2012

Description

SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.

Required Modules

modules documentation

Serial

soapdenovo-trans

System Variables

HPC_{{#uppercase:soapdenovo-trans}}_DIR - installation directory
HPC_SOAPDENOVOTRANS_BIN - directory where SOAPdenov-Trans binaries are located

@@ Line 1: / Line 1: @@
 [[Category:Software]]
 {|<!--CONFIGURATION: REQUIRED-->
@@ Line 5: / Line 4: @@
 |{{#vardefine:url|http://soap.genomics.org.cn/SOAPdenovo-Trans.html}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
-|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
-|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 |{{#vardefine:exe|}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
@@ Line 23: / Line 19: @@
 SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==}}
+==Required Modules==
-To use SOAPdenovo-Trans with the environment modules system at HPC the following commands are available:
+[[Modules|modules documentation]]
+===Serial===
-Get module information for soapdenovo-trans:
+*{{#var:app}}
- $module spider soapdenovo-trans
-Load the default application module:
- $module load soapdenovo-trans
-The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
-    HPC_SOAPDENOVOTRANS_DIR - directory where SOAPdenovo-Trans is located.
-    HPC_SOAPDENOVOTRANS_BIN - directory where SOAPdenov-Trans binaries are located
 ==System Variables==
 * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
-<!--Run-->
+* HPC_SOAPDENOVOTRANS_BIN - directory where SOAPdenov-Trans binaries are located
+<!--Additional-->
-{{#if: {{#var: exe}}|==How To Run==
+{{#if: {{#var: exe}}|==Additional Information==
 DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
 |}}