Difference between revisions of "WU BLAST"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|wublast}} | |{{#vardefine:app|wublast}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|http://blast.wustl.edu/}} |
| − | <!--CONFIGURATION: OPTIONAL (|1}} | + | <!--CONFIGURATION: OPTIONAL (1=ON)--> |
| − | |{{#vardefine: | + | |{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED--> |
| − | |{{#vardefine:exe|}} | + | |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> |
| − | |{{#vardefine: | + | |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> |
| − | |{{#vardefine:policy|}} | + | |{{#vardefine:exe|}} <!--RUNNING --> |
| − | |{{#vardefine:testing|}} | + | |{{#vardefine:conf|}} <!--CONFIGS--> |
| − | |{{#vardefine:faq|}} | + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> |
| − | |{{#vardefine:citation|}} | + | |{{#vardefine:policy|}} <!--POLICY--> |
| + | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
| + | |{{#vardefine:faq|}} <!--FAQ--> | ||
| + | |{{#vardefine:citation|}} <!--CITATION--> | ||
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
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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}}}}|}} | ||
| − | + | WU-Blast is the former Washington University BLAST now provided by the Advanced Biocomputing, LLC. | |
| + | * most sensitive, fastest and flexible core BLAST engine — target your searches easier and get better results faster | ||
| + | * faster, easier and more robust database management — faster updates leave more time to analyze; robust error checking identifies problems sooner; flexible identifiers improve pipeline design and management | ||
| + | * long-term consistent behavior—drop-in upgrades for over 15 years—avoids wholesale retraining of staff and retuning of analysis pipelines, reduces errors and saves time | ||
| + | * up to twice as fast as NCBI BLAST, yet more sensitive and robust | ||
| + | * no special/expensive hardware requirements or usage restrictions | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Required Modules== |
| − | + | [[Modules|modules documentation]] | |
| + | ===Serial=== | ||
| + | *{{#var:app}} | ||
| + | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | <!--Run--> | ||
| + | |||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
| + | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#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. | ||
|}} | |}} | ||
| − | <!-- | + | <!--PBS scripts--> |
| − | {{#if: {{#var: | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | See the [[{{PAGENAME}} | ||
| − | |}} | ||
<!--Policy--> | <!--Policy--> | ||
{{#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) | |
| − | WRITE USAGE POLICY HERE ( | ||
| − | |||
|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | + | DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE | |
| − | |||
| − | |||
|}} | |}} | ||
<!--Faq--> | <!--Faq--> | ||
| Line 57: | Line 62: | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | DOUBLE_CLICK_TO_WRITE_CITATION_HERE | |
| − | |||
| − | |||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
{{#if: {{#var: installation}}|==Installation== | {{#if: {{#var: installation}}|==Installation== | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
| − | |||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 19:50, 27 May 2022
Description
WU-Blast is the former Washington University BLAST now provided by the Advanced Biocomputing, LLC.
- most sensitive, fastest and flexible core BLAST engine — target your searches easier and get better results faster
- faster, easier and more robust database management — faster updates leave more time to analyze; robust error checking identifies problems sooner; flexible identifiers improve pipeline design and management
- long-term consistent behavior—drop-in upgrades for over 15 years—avoids wholesale retraining of staff and retuning of analysis pipelines, reduces errors and saves time
- up to twice as fast as NCBI BLAST, yet more sensitive and robust
- no special/expensive hardware requirements or usage restrictions
Required Modules
Serial
- wublast
System Variables
- HPC_WUBLAST_DIR - installation directory
Validation
- Validated 4/5/2018