Difference between revisions of "Gmap"

Latest revision as of 17:11, 15 August 2022

Description

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

Environment Modules

Run module spider gmap to find out what environment modules are available for this application.

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 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]]
-<!-- ########  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 ######## -->
@@ Line 35: / Line 20: @@
 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
 GSNAP: Genomic Short-read Nucleotide Alignment Program
+<!--Modules-->
-==Available versions==
+==Environment Modules==
-* 20070928 (used by [[PASA]]).
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 20120703, available on both EL5 and EL6.
+==System Variables==
-* 20120712 (default), available on both EL5 and EL6.
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!-- -->
-{{#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>/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.
+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.
+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: conf}}|==Configuration==
@@ Line 51: / Line 37: @@
 {{#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 58: / Line 44: @@
 *'''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
 |}}