Difference between revisions of "Main Page"
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A cluster is a shared resource with different users running different types of analyses. Nearly all clusters use a piece of software called a queue manager to fairly share out the resource. The queue manager on marvin is called Grid Engine, and it has several commands available, all beginning with '''q''' and with '''qsub''' being the most commonly used as it submits a command via a jobscript to be processed. Here are some tips: | A cluster is a shared resource with different users running different types of analyses. Nearly all clusters use a piece of software called a queue manager to fairly share out the resource. The queue manager on marvin is called Grid Engine, and it has several commands available, all beginning with '''q''' and with '''qsub''' being the most commonly used as it submits a command via a jobscript to be processed. Here are some tips: | ||
* [[Queue Manager Tips]] | * [[Queue Manager Tips]] | ||
| + | * [[General Command-line Tips]] | ||
= Data Examples = | = Data Examples = | ||
Revision as of 12:43, 8 November 2016
Contents
Usage of Cluster
Documented Programs
- abacas
- augustus
- BamQC
- BLAST
- blast2go: b2g4pipe
- bowtie2
- BUSCO
- CAFE
- cd-hit
- cegma
- diamond
- ensembl
- FASTQC and MultiQC
- Archaeopteryx and Forester
- GapFiller
- gubbins
- JBrowse
- kallisto
- multiqc
- MUMmer
- OrthoFinder
- PGAP
- prokka
- pyrad
- python
- rnammer
- RAxML
- samtools
- SPAdes
- sra-tools
- srst2
- SSPACE
- stacks
- trimmomatic
- velvet
Queue Manager Tips
A cluster is a shared resource with different users running different types of analyses. Nearly all clusters use a piece of software called a queue manager to fairly share out the resource. The queue manager on marvin is called Grid Engine, and it has several commands available, all beginning with q and with qsub being the most commonly used as it submits a command via a jobscript to be processed. Here are some tips:
Data Examples
Procedures
(short sequence of tasks with a certain short-term goal, often, a simple script)
Explanations
Pipelines
(Workflow with a specific end-goal)
Protocols
(Extensive workflows with different with several possible end goals) Synthetic Long reads
Cluster Administration
- Admin Tips
- RedHat
- Globus_gridftp
- Galaxy Setup
- Son of Gridengine
- Blas Libraries
- CMake
- Users and Groups
- node1 issues
- 6TB storage expansion
- Frontend Restart
- environment-modules
- H: drive on cluster
- Incident: Can't connect to BerkeleyDB
- Bioinformatics Wordpress Site
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Directory Organization Exercise
- Glossary
- Key Bindings
- Cheatsheets
