Difference between revisions of "Tgicl"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
 
(14 intermediate revisions by 2 users not shown)
Line 4: Line 4:
 
|{{#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-->
+
|{{#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-->
 
|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
Line 19: Line 16:
 
<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 +
 
 
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==
+
==Required Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
[[Modules|modules documentation]]
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+
===Serial===
* HPC_TGICL_DIR - installation directory
+
*{{#var:app}}
 +
==System Variables==
 +
* 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
 
+
<!--Additional-->
===Note:===
+
{{#if: {{#var: exe}}|==Additional Information==
By default loading the module for tgicl also loads the latest Perl and CAP3 modules. The main version of cap3 is used for analyses. If you wish to use the cap3 version distributed with tgicl, it is located at $HPC_TGICL_BIN/cap3.tgicl
+
* To copy the default skeleton configuration file to the working directory:
 
+
cp $HPC_TGICL_CONF/tgicl.cfg .
<!--Run-->
+
* Sample run
{{#if: {{#var: exe}}|==How To Run==
+
tgicl -F sample.fasta  -q sample.qual -c 4
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
 
 
|}}
 
|}}
 
<!--Configuration-->
 
<!--Configuration-->
Line 53: Line 45:
 
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==
+
{{#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