Difference between revisions of "UCSC"
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Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
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__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | {| | + | |{{#vardefine:app|ucsc}} |
| − | <!--Main settings - REQUIRED--> | ||
| − | |{{#vardefine:app| | ||
|{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}} | |{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}} | ||
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| − | |||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#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--> | ||
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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 --> |
|} | |} | ||
<!-- ######## Template Body ######## --> | <!-- ######## Template Body ######## --> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | USCS genome browser utilities include programs for sorting, splitting (faSpli), or merging fasta sequences; record parsing and data conversion using GenBank, fasta, nib, and blast data formats; sequence alignment; motif searching; hidden Markov model development; and much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed graphs to developing routines for SQL, HTML, or CGI code. Additional library functions are available for biological sequence and data manipulation tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loading, and manipulating data in the UCSC Genome Browser Databases. | |
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{{app}}} you have to cite it as follows: | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| − | + | ||
| + | http://genome.ucsc.edu/. | ||
|}} | |}} | ||
Latest revision as of 20:53, 12 August 2022
Description
USCS genome browser utilities include programs for sorting, splitting (faSpli), or merging fasta sequences; record parsing and data conversion using GenBank, fasta, nib, and blast data formats; sequence alignment; motif searching; hidden Markov model development; and much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed graphs to developing routines for SQL, HTML, or CGI code. Additional library functions are available for biological sequence and data manipulation tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loading, and manipulating data in the UCSC Genome Browser Databases.
Environment Modules
Run module spider ucsc to find out what environment modules are available for this application.
System Variables
- HPC_UCSC_DIR - installation directory
Citation
If you publish research that uses {{{app}}} you have to cite it as follows: