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Usage of Cluster
Documented Programs
The following can be seen as extra notes referring to these programs usage on the marvin cluster, with an emphais on example use-cases. Most, if not all, will have their own special websites, with more detailed manuals and further information.
| * abacas | * albacore | * ariba | * aspera | * assembly-stats | * augustus |
| * BamQC | * bamtools | * bcftools | * bedtools | * bgenie | * BLAST |
| * Blat | * blast2go: b2g4pipe | * bowtie | * bowtie2 | * bwa | * BUSCO |
| * CAFE | * canu | * cd-hit | * cegma | * clustal | * cramtools |
| * deeptools | * detonate | * diamond | * ea-utils | * ensembl | * ETE |
| * FASTQC and MultiQC | * Archaeopteryx and Forester | * GapFiller | * GenomeTools | * gubbins | * JBrowse |
| * kallisto | * kentUtils | * last | * lastz | * macs2 | * Mash |
| * mega | * MUMmer | * NanoSim | * OrthoFinder | * PGAP | * picard-tools |
| * poRe | * poretools | * prokka | * pyrad | * python | * qualimap |
| * quast | * R | * RAxML | * Repeatmasker | * rnammer | * roary |
| * RSeQC | * samtools | * Satsuma | * sickle | * SPAdes | * sra-tools |
| * srst2 | * SSPACE | * stacks | * Thor | * Tophat | * trimmomatic |
| * Trinity | * t-coffee | * 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)
- Trinity_Protocol
- STAR BEAST
- callSNPs.py
- mapping.py
- Edgen RNAseq
- Miseq Prokaryote FASTQ analysis
- snpcallphylo
- Bottlenose dolphin population genomic analysis
- ChIP-Seq Top2 peak-calling
Protocols
(Extensive workflows with different with several possible end goals)
- Synthetic Long reads
- MinION (Oxford Nanopore)
- MinKNOW folders and log files
- Research Data Management
Cluster Administration
- Hardware Issues
- Admin Tips
- RedHat
- Globus_gridftp
- Galaxy Setup
- Son of Gridengine
- Blas Libraries
- CMake
- Users and Groups
- emailing
- biotime machine
- node1 issues
- 6TB storage expansion
- Home directories max-out incident 28.11.2016
- Frontend Restart
- environment-modules
- H: drive on cluster
- Incident: Can't connect to BerkeleyDB
- Bioinformatics Wordpress Site
- Backups
- Python DRMAA
- SAN disconnect incident 10.01.2017
- Memory repair glitch 16.02.2017
- node9 network failure incident 16-20.03.2017
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Biolinux Source course
- Directory Organization Exercise
- Glossary
- Key Bindings
- one-liners
- Cheatsheets
- Links
- pandoc modified manual
- Command Line Exercises
hdi2u
The half-day linux course held on 20th April. Modified version of I2U4BGA.
RNAseq for DGE
- Theoretical background
- Quality Control and Preprocessing
- Mapping to Reference
- Mapping Quality Exercise
- Key Aspects of using R
- Estimating Gene Count Exercise
- Differential Expression Exercise
- Functional Analysis Exercise
