Difference between revisions of "Cactus"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|cactus}} |{{#vardefine:url|https://github.com/ComparativeGenomicsToolkit/cac...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|cactus}} | |{{#vardefine:app|cactus}} | ||
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | + | |{{#vardefine:job|1}} <!--JOB SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| − | * HPC_{{uc:{{#var:app}}}}_BIN - | + | * HPC_{{uc:{{#var:app}}}}_BIN - executables directory |
<!--Configuration--> | <!--Configuration--> | ||
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<!--Job Scripts--> | <!--Job Scripts--> | ||
{{#if: {{#var: job}}|==Job Script Examples== | {{#if: {{#var: job}}|==Job Script Examples== | ||
| + | Using the [https://github.com/ComparativeGenomicsToolkit/cactus#running-step-by-step "step-by-step" procedure] with "cactus-prepare" has proven to be the most successful way to run the Cactus workflow on HiPerGator. | ||
| + | |||
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples. | See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples. | ||
|}} | |}} | ||
Latest revision as of 21:30, 18 March 2024
Description
Cactus is a reference-free whole-genome multiple alignment program. Please cite the Progressive Cactus paper when using Cactus. Additional descriptions of the core algorithms can be found here and here.
Environment Modules
Run module spider cactus to find out what environment modules are available for this application.
System Variables
- HPC_CACTUS_DIR - installation directory
- HPC_CACTUS_BIN - executables directory
Job Script Examples
Using the "step-by-step" procedure with "cactus-prepare" has proven to be the most successful way to run the Cactus workflow on HiPerGator.
See the Cactus_Job_Scripts page for cactus Job script examples.
Citation
If you publish research that uses cactus you have to cite it as follows:
https://www.nature.com/articles/s41586-020-2871-y