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Runtime Environments for FGI grid

Several tools and applications are installed to the FGI grid environment by the administrators. To use these tools, users have to define the required runtime environment or run time environments that the task needs. When a runtime environment is defined in the job description file (.xrsl file) then job only those computing clusters, that contain the required runtime environment, accept the task. 

When the grid computing task starts in some of the computing clusters, runtime environment is used to automatically set up command paths and environment variables, that the selected software or tool requires.

Below are listed the available runtime environments in the FGI environment.

Information about how to use different tools in FGI can be found form the corresponding ARC instructions page

AMBER

Name: APPS/CHEM/AMBER-12
Description: Amber is a versatile molecular dynamics software
Usage: ARC instructions
Available: FGI

AutoDock

Name: APPS/CHEM/AUTODOCK
Description: Flexible ligand docking tool
Usage: ARC instructions
Available: FGI

BLAST

Name: APPS/BIO/BLAST+-2.2.28
Description: NCBI BLAST sequence similarity search tool
Usage: ARC instructions
Available: FGI

Bowtie 0.12.7 and 2.0.5

Name: APPS/BIO/BOWTIE-0.12.7
Name: APPS/BIO/BOWTIE-2.0.0
Description: Bowtie sort read mapping tool
Usage: ARC instructions for BOWTIE-0.12.7  ARC instructions for BOWTIE-2.0.5
Available: FGI

BWA

Name: APPS/BIO/BWA-0.6.1
Description: BWA sort read mapping tool
Usage: ARC instructions 
Available: FGI

Name: APPS/BIO/CUFFLINKS-1.3.0/2.1.1
Description: Cufflinks
Usage: ARC instructions
Available: FGI

Elmer

EMBOSS

Name: APPS/BIO/EMBOSS-6.4.0
Description: EMBOSS sequence analysis tool kit
Usage: ARC instructions
Available: FGI

Exonerate

Name: APPS/BIO/EXONERATE-2.2.0
Description: General sequence alignment tool
Usage: ARC instructions
Available: FGI

FreeSurfer

Name: APPS/IMAG/FREESURFER
Description: Image processing tool structural brain MRI data
Usage: ARC instructions
Available: FGI

Gromacs

Name: APPS/CHEM/GROMACS-4.5.5
Description: Molecular dynamics program
Usage: ARC instructions
Available: FGI

GPAW

Name: APPS/PHYS/GPAW-0.9
Description: Program package for electronic structure calculations
Usage: ARC instructions
Available: FGI

GSNAP

Name: APPS/BIO/GSNAP
Description: Short read aligner for NGS data
Usage: ARC instructions
Available: FGI

HMMER 3.0

Name: APPS/BIO/HMMER-3.0
Description: HMMER analysis tool
RE Homepage: ARC instructions   
Available: vuori-arc.csc.fi

Interproscan5

Name: APPS/BIO/INTERPROSCAN-5-44.0
Description: InterProScan protein motif search tool
RE Homepage: ARC instructions
Available: usva.fgi.csc.fi

NAMD

Name: APPS/CHEM/NAMD-2.9
Description: NAMD molecular dynamics engine
RE Homepage: ARC instructions
Available: FGI

MISO 

Name: APPS/BIO/MISO-0.4.7
Description: Program to identify differentially regulated isoforms or exons from RNA-seq data.
Usage: ARC instructions

Available: FGI

Matlab Compiler Runtime

Name: APPS/MATH/MCR-R2013A
Description: C library for executing C converted Matlab codes
Usage: ARC instructions
Available: FGI

MrBayes

Name: APPS/BIO/MRBAYES-3.2.1
Description: Program for inferring phylogenies using bayesian methods
Usage: ARC instructions
Available: FGI

ORCA

Name: APPS/CHEM/ORCA-2.9.1
Description: Quantum chemistry
Usage: ARC instructions
Available: FGI

R-3.0.2

Name: APPS/STATISTICS/R-3.0.2
Description: R statistics package
Usage: ARC instructions
Available: FGI

SAMtools

Name: APPS/BIO/SAMTOOLS
Description: SAMtools sequence analysis tool
Usage: ARC instructions
Available: FGI

SHRiMP

Name: APPS/BIO/SHRIMP-2.2.2
Description: SHRIMP sequence analysis tool
RE Homepage:https://extras.csc.fi/mgrid/shrimp_re/
Available: FGI

TopHat

Name: APPS/BIO/TOPHAT-1.3.2 and APPS/BIO/TOPHAT-2.0.6
Description: TopHat- splice junction mapper for RNA-Seq reads
Usage: ARC instructions
Available: FGI

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