Difference between revisions of "Gmap"

Revision as of 19:19, 11 February 2021

Description

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

Required Modules

modules documentation

Serial

gmap

System Variables

HPC_GMAP_DIR - installation directory
HPC_GMAP_BIN - executable directory.

How To Run

The default shared Genome Database location is /data/reference/gmap. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.

If you are using an older gmap module the reference directory path could be wrong in which case you can specify the path with the '-D' argument.

Make sure to request two additional processors by increasing the "ppn" in the job script accordingly when running with the "-t X" argument to enable multi-threaded execution. When "-t" is used Gmap will create two more processes than the number of threads set with "-t", which will interfere with other people's jobs on the server gmap is running on and could result in the offending user's account being disabled.

Citation

If you publish research that uses gmap you have to cite it as follows:

Thomas D. Wu and Colin K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21:1859-1875

Thomas D. Wu and Serban Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 2010 26:873-881

@@ Line 2: / Line 2: @@
 __NOEDITSECTION__
 [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|gmap}}
 |{{#vardefine:url|http://research-pub.gene.com/gmap/}}
-<!--Compiler and MPI settings - OPTIONAL -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 |{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 26: / Line 11: @@
 |{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 |{{#vardefine:faq|}} <!--Enable FAQ section -->
-|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
+|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 |}
 <!-- ########  Template Body ######## -->
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
 GSNAP: Genomic Short-read Nucleotide Alignment Program
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Required Modules==
-==Available versions==
+[[Modules|modules documentation]]
-* 20070928 (used by [[PASA]]).
+===Serial===
-* 20120111.
+*{{#var:app}}
-* 20120323.
+==System Variables==
-* 20120427.
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* 20120524
-* 20120612 (default).
-<!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_GMAP_BIN - executable directory.
+{{#if: {{#var: exe}}|==How To Run==
+The default shared Genome Database location is <code>/data/reference/gmap</code>. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.
+If you are using an older gmap module the reference directory path could be wrong in which case you can specify the path with the '-D' argument.
-'''Note: perl/5.14.1 and samtools/0.1.18" modules are automatically loaded for GMAP/GSNAP 20120323.
+Make sure to request two additional processors by increasing the "ppn" in the job script accordingly when running with the "-t X" argument to enable multi-threaded execution. When "-t" is used Gmap will create two more processes than the number of threads set with "-t", which will interfere with other people's jobs on the server gmap is running on and could result in the offending user's account being disabled.
-{{#if: {{#var: exe}}|==How To Run==
-The default shared Genome Database location is <code>/project/bio/gmap</code>. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.
 |}}
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 56: / Line 39: @@
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#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)|}}
 {{#if: {{#var: testing}}|==Performance==
@@ Line 63: / Line 46: @@
 *'''Q:''' **'''A:'''|}}
 {{#if: {{#var: citation}}|==Citation==
-If you publish research that uses {{{app}}} you have to cite it as follows:
+If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE CITATION HERE
+Thomas D. Wu and Colin K. Watanabe
+GMAP: a genomic mapping and alignment program for mRNA and EST sequences
+Bioinformatics 2005 21:1859-1875
+Thomas D. Wu and Serban Nacu
+Fast and SNP-tolerant detection of complex variants and splicing in short reads
+Bioinformatics 2010 26:873-881
 |}}