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Usage of Cluster

Cluster Manual Available Software

Documented Programs

• abacas
• augustus
• BamQC
• BLAST
• blast2go: b2g4pipe
• bowtie2
• BUSCO
• CAFE
• cd-hit
• cegma
• diamond
• ensembl
• FASTQC and MultiQC
• 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:

• Queue Manager Tips

Data Examples

• Two Eel Scaffolds

Procedures

(short sequence of tasks with a certain short-term goal, often, a simple script)

• Calculating coverage

Navigating genomic data websites

• Patric
• NCBI

File format expalanations

• VCF

Pipelines

(Workflow with a specific end-goal)

• Trinity_Protocol
• STAR BEAST
• callSNPs.py
• Edgen RNAseq
• Miseq Prokaryote FASTQ analysis
• snpcallphylo

Protocols

(Extensive workflows with different with several possible end goals) Synthetic Long reads

Cluster Administration

• Admin Tips
• RedHat
• Globus_gridftp
• Galaxy Setup
• 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