Difference between revisions of "Gmap"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:Genomics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the v...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|gmap}} | |{{#vardefine:app|gmap}} | ||
|{{#vardefine:url|http://research-pub.gene.com/gmap/}} | |{{#vardefine:url|http://research-pub.gene.com/gmap/}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
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|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
|{{#vardefine:faq|}} <!--Enable FAQ section --> | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| − | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | + | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> |
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<!-- ######## Template Body ######## --> | <!-- ######## Template Body ######## --> | ||
<!--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}}}}|}} |
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GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and | ||
GSNAP: Genomic Short-read Nucleotide Alignment Program | GSNAP: Genomic Short-read Nucleotide Alignment Program | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
| − | < | ||
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| − | {{ | ||
* HPC_GMAP_BIN - executable directory. | * HPC_GMAP_BIN - executable directory. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#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. | |
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| + | 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== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#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)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{ | + | If you publish research that uses {{#var:app}} 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 | ||
|}} | |}} | ||
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