Difference between revisions of "Tgicl"

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(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|tgicl}} |{{#vardefine:url|http://compbio.dfci.harvard.edu/tgi/software/}} <!--CONFIGURATION: OPTIONAL (1=...")
 
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|{{#vardefine:url|http://compbio.dfci.harvard.edu/tgi/software/}}
 
|{{#vardefine:url|http://compbio.dfci.harvard.edu/tgi/software/}}
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
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|{{#vardefine:exe|1}} <!--RUNNING -->
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 
|{{#vardefine:exe|}} <!--RUNNING -->
 
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
 
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets
 
TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets
  
 
This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
 
This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
 
<!--Location-->
 
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
<!--Versions-->
 
==Available versions==
 
* 2.1
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
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==Required Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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[[Modules|modules documentation]]
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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===Serial===
* HPC_TGICL_DIR - installation directory
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*{{#var:app}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_TGICL_BIN - executable directory
 
* HPC_TGICL_BIN - executable directory
* HPC_TGICL_LIB - lib directory
 
 
* HPC_TGICL_CONF - conf directory
 
* HPC_TGICL_CONF - conf directory
<!--Run-->
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<!--Additional-->
{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: exe}}|==Additional Information==
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
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* To copy the default skeleton configuration file to the working directory:
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cp $HPC_TGICL_CONF/tgicl.cfg .
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* Sample run
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tgicl -F sample.fasta  -q sample.qual -c 4
 
|}}
 
|}}
 
<!--Configuration-->
 
<!--Configuration-->
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
|}}
 
|}}

Latest revision as of 21:29, 6 December 2019

Description

tgicl website  

TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets

This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3

Required Modules

modules documentation

Serial

  • tgicl

System Variables

  • HPC_TGICL_DIR - installation directory
  • HPC_TGICL_BIN - executable directory
  • HPC_TGICL_CONF - conf directory

Additional Information

  • To copy the default skeleton configuration file to the working directory:
cp $HPC_TGICL_CONF/tgicl.cfg .
  • Sample run
tgicl -F sample.fasta  -q sample.qual -c 4