Difference between revisions of "UCSC"

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:

http://genome.ucsc.edu/.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
+|{{#vardefine:app|ucsc}}
-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|kent}}
 |{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}}
-<!--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|}} <!--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 33: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-Kent source utilities are based on the code originally developed by Jim Kent for the UCSC genome browser. They include programs for sorting, splitting, 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.
+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.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Available versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 20120423
+==System Variables==
-<!-- -->
+* 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}}}}|}}
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
@@ Line 47: / Line 30: @@
 {{#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 55: / Line 38: @@
 {{#if: {{#var: citation}}|==Citation==
 If you publish research that uses {{{app}}} you have to cite it as follows:
-WRITE CITATION HERE
+http://genome.ucsc.edu/.
 |}}