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List of Atmosphere Images

This is a list of the images that are available in Atmosphere.

Filtration is disabled as no filters are defined.

Filter is off as no table is provided.

Image Name

Description

Tags

acesar RNA-Seq analysis

acesar RNA-Seq analysis

 

Agalma v.1

Agalma, HiSeq transcriptome processing pipeline by Casey Dunn et.al.

 

agave docker

Snapshot of a docker instance configured to be run by agave.

 

aki-ubuntu 12.04 3.13.0-35-generic (trusty)

aki-ubuntu 12.04 3.13.0-35-generic (trusty)

 

Angstrom VM v2

ea632bc6-0bfa-47d6-ad00-67310df9001d

 

ari-ubuntu 12.04 3.13.0-35-generic (trusty)

ari-ubuntu 12.04 3.13.0-35-generic (trusty)

 

BASE_IMAGE

This is the base image with all Python libraries installed

Python2.7, gwas

BATools 0.0.1

BATools 0.0.1

 

binilbenjamin Master

binilbenjamin Master

 

binilbenjamin Slave

binilbenjamin Slave

 

BioClassRoom v2.1

This image provides software for teaching basic bioinformatics including Komodo Edit 8, BioEdit, and BioPerl

BioPerl, Unity, Ubuntu, komodoedit, wine, bioedit

BioClassRoom v 2.2

This image provides software for teaching basic bioinformatics including Komodo Edit 8, BioEdit, and BioPerl

BioPerl, Unity, Ubuntu, komodoedit, wine, bioedit

Bioinformatic_tool_python

Similar as mfc Maloof Bioinfv6 with python3.3, numpy and some of the newest R package for ChIP-seq analysis

 

bisque-engine

This is a simple bisque engine to be used for module integration

 

bq Engine sabrinanusrat 1

Working installation of bisque engine server. Running nginx and uwsgi.

 

Canberra List Rank spt6655 V1

Configuration of BASE_IMAGE with mlpy and its dependencies installed. Canberra distance app is also installed, along with example data. The documentation for the Canberra program can be found here: https://pods.iplantcollaborative.org/wiki/display/DEapps/Canberra+Distance

Python2.7, python

CentOS 5.8 - iPlant Base 2014

CentOS 5.8 - iPlant Base 2014

 

CentOS 5.8 JLAMP Server

CentOS 5.8 JLAMP Server

 

Centos 6.3 NoGui 4GB 64-bit

ab71a2b1-fc15-4365-bfd2-21fe2edf76df

centos

Centos 6.5 Gnome Desktop Prep1

Centos 6.5 Gnome Desktop Prep1

 

CGS-IU-v1.0

CGS-IU-v1.0

 

ChipSeq

emi-0BEB20AD

 

CKAN-Image

Ckan development instance

ckan, geoserver

CKAN-Image

Ckan development instance

ckan, geoserver

Cleared Leaf Demo Site

Demo site for the Cleared Leaf DB.

 

Comp Bac Genomics Williams 1.2

This images comes with several tools useful for comparative bacterial genomics

artemis, BioPerl, brig, FastQC, FastX, ksnp, mauve, Velvet, ncbi-blast

Comp Bac Genomics Williams 1.4

This images comes with several tools useful for comparative bacterial genomics

artemis, BioPerl, brig, FastQC, FastX, ksnp, mauve, Velvet, ncbi-blast, PandaSeq

CoreOS

CoreOS

 

CropDatafarm

A packaged web database for storing and analyzing crop phenotype and genotype data.

T3, mysql, R, git, apache2, Ubuntu, triticeae_toolbox, php, postfix

dailybob

9a09ca34-da50-45a5-a877-be44b3bfa197

 

DF_qtlhmm_PIF

Apart from what's in Maloof08-v2, this image has HMMER3, software for gene tree – species tree reconciliation, HyPhy, StochHMM C++ library, and HMM and other libraries needed to run DART's ProtPal, XRate, and HandAlign.

 

DoaneUbuntu01

This image is set up for doing image processing with Python

Ubuntu, Python2.7

DoaneUbuntu01

This image is set up for doing image processing with Python

Ubuntu, Python2.7

Entangled Genomes 08/10/2012

Metagenomics and NGS viewer VM for OSU

NGS, Metagenomics

EpitopeAnalysis_1

This image has some programs installed onto the Ubuntu 12.04 - iPlant image. The following programs are installed: Blast (for comparing biological sequences), Clustal Omega (for aligning biological sequences), Meme Suite (for finding motifs in biological sequences), Sun Java, and Eclipse Java IDE. This image can use VNC.

vnc, Ubuntu, MEME, glam2, mast, eclipse, BLAST, clustal, omega

EpitopeAnalysis_2

This comes with blast, the meme suite, and clustal omega all pre-installed

 

GCAT_Assembly2_CW1

denovo assembler; Whole genome shotgun assembler on Centos 6

centos6, ray, allpathslg

GCAT_Assembly2_CW1

denovo assembler; Whole genome shotgun assembler on Centos 6

centos6, ray, allpathslg

GCAT_VariantDiscovery

Stacks tools

 

GCATAssembly1_CW

Jellyfish, Quake, and SOAPdenovo2 assembly tools

R, soapdenovo, jellyfish, quake

GEMMA 0.94

GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS).

gemma

Grinder-0.5.3

This instance contains a command-line implementation of Grinder. Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

grinder, shotgun, amplicon

Hall-lab-v1

Hall-lab-v1

Python2.7, matlab-mcr

HypoTrace

HypoTrace

 

HYPOTrace v2

HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis. Version 2 fixes a permissions problem with the hypotrace binary.

Matlab, hypotrace

IBP Workbench v5 09/13/2012

This image contains a preliminary version of the IBP Workbench tool intended for remote access without having to install it on a local workstation. Working tools include the IBP Workbench itself, the Germplasm Browser, the Study Browser, and the GDMS. The other breeding tools are native only to Windows and therefore cannot be integrated with this Linux image. Only the Chickpea IBDB database is available for this version of the Workbench.

GCP, IBP, Workbench, ibpworkbench, efficio, Featured

Image Processing Toolkit v3 08/23/2012

Image Processing Toolkit v3 08/23/2012

 

Image Processing Toolkit v4

Contains suite of image processing programs for image based phenotyping.

 

Image Processing Toolkit v5

emi-99433292

R

Image Processing Toolkit v6

non-steady state kinematics analysis of root growth, provides growth velocity and REGR pattern as well as values for length of elongation zone and magnitude and position of max strain rates

Kinematics

iPlant Base Image w VNC (04/21/2012)

iPlant Base Image w VNC updated 04-21-2012, RHEL 5.8

 

iPlant Centos 6.5 NoGUI Base3

iPlant Centos 6.5 NoGUI Base

centos, centos6, nodesktop, nogui, base, Featured

iPlant Datastore Public Files

The iPlant Datastore Web Interface (as is running at http://mirrors.iplantc.org/).

 

ivilab-setup_predoehl_01

Ubuntu plus all the development packages (lots of *-dev packages!) and docs needed to compile and run IVILAB software. However, it does not contain the IVILAB library or build system (Make), since they are not deb packages.

Ubuntu, ivilab

ivilab-setup_predoehl_02

Ubuntu 12.04-based image with all the *-dev packages (free SW from ubuntu repositories) required for source-based development using IVILAB research code.

Ubuntu, ivilab

jDuvick xGDBvm-gamma5b (vdeleted 2014-02-10)

70ae6738-2276-41a2-950c-b5c24479b61b

 

KBase 2013-06-04

b49096fe-74b2-4720-b8c7-f6ff20f658d2

 

khmer-machine-jeramia-v03

khmer-machine-jeramia-v03

 

KOBAS 2.0-09052014

This Atmosphere image is a build of KOBAS 2.0, which is an update of KOBAS (KEGG Orthology Based Annotation System). Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases.KOBAS 2.0 integrates information from the Gene Ontology (GO), KEGG Pathways, Pathway Interaction Database (PID, including BioCarta pathways), Reactome, BioCyc, and PANTHER pathways and disease databases (including OMIM, KEGG DISEASE, FunDO, GAD, and NHGRI GWAS Catalog disease). KOBAS 2.0 can annotate queries to either KEGG genes or KEGG Orthology (KO) terms.This image will come pre loaded with human annotation datasets, as well as the KEGG orthology. To import additional datasets, please run the select_org command upon launching. You can then view a list of available databases or just enter the KOBAS abbreviation for the databases to import new datasets. The command will create the appropriate blast databases for you. Documentation on usage and an example tutorial can be found at this link: https://pods.iplantcollaborative.org/wiki/display/atmman/KOBAS+2.0

go, pathway_analysis, functional_enrichment, annotate

LBL NGS v3.1

LBL NGS v3.1

 

LBNL NGS v3.0

LBNL NGS v3.0

 

lluviaflores GATKPinyon lluviaflores v3

lluviaflores GATKPinyon lluviaflores v3

 

MAKER with workqueue

MAKER 2.28 with workqueue and workers

MAKER

MAKER-P_2.28

 

MAKER, maker-p, maker-p-228

MAKER-P_2.31.3

MAKER-P version 2.31.3 provides an automated pipeline and tool-set for annotating protein-coding and non-coding genes along genome assemblies. This installation is MPI-enabled to utilize instances with multiple CPUs. Also installed is wq_maker, a wrapper that uses the Work Queue framework for distributed execution on available resources. A tutorial for using this image is available here: https://pods.iplantcollaborative.org/wiki/display/sciplant/MAKER-P+Atmosphere+Tutorial. This image is an update of prior image (6c7d-4cd5-bfef-06df3482de0a) to include Augustus.

AUGUSTUS, BLAST, blat, RepeatMasker, exonerate, SNAP, maker-p, wq_maker

MAKER-P_2.31.3-07 resize

MAKER-P_2.31.3-07 resize

 

Maloof07

Maloof07

 

Maloof08 v2

Tools for bioinformatics analysis, with a focus on short read sequencing data, statistical analysis in R, and phylogenetics. Contains most software in currently in use in the Maloof Lab. Installation notes at https://bitbucket.org/jnmaloof/atmosphereimages

Featured

Maloof BioInf v6 08/22/2012

emi-9394226D

 

MolecularEvolution2013

Software used at the 2013 Marine Biological Laboratory Molecular Evolution workshop. Useful for multiple sequence alignment, phylogenetic and coalescent analyses.

R

MrBayes with TreeMix

MrBayes with TreeMix

 

NAUTools IV

Tools for the Pinyon Pine Project at Northern Arizona University

Ubuntu, QIIME, vnc, R, python, beagle, IGV, vcftools, stacks, bwa, GATK, picard, SAMtools, bowtie2, Bowtie, ea-utils, r-studio-server

NAUTools v III

NAUTools v III

 

New CBSU Workshop Image (11/04/2011)

CBSU Workshop Image - 11/04/2011

 

NGS Viewers v3.2 (03-15-2013)

Now includes IGB ver 7.0.1. Updated NGS Viewers

NGS, Featured

NGS Viewers v3.2 NOMAC

NGS Viewers v3.2 NOMAC

 

NGS-pu

Tools installed for NGS assembly and analysis. Software installed: samtools, geany, bowtie2, bwa, mauve, bedtools, fastxtoolkit, raxml, beast v1.7.4, tracer v1.5.

NGS-pu3

NGS-pu3

 

NGS-pu4

NGS-pu4

 

Ontologizer

Ontologizer

 

ORIM VNC alpha_v_0.9

Connect to the image using VNC and launch firefox. Navigate to 'localhost' in the browser.The purpose of the ORtholog Interval Mining tool (ORIM) is to permit researchers to identify orthologous candidate genes between species. The orthologous candidate genes can be located by searching an organism's entire genome, or by searching in particular intervals, which are specified using the physical base pair positions on the chromosome. In addition to filtering by position in the genome, the candidate genes can be sorted by whether or not the candidate gene is reciprocally a best BLAST hit. The plant genomes and annotation data are sourced from Phytozome, with additional annotations from various other sources.In addition to allowing the user to compare a handful few intervals of interest manually, the software also allows for bulk comparison for larger scale exploration of the genomes. The result of comparing intervals is a table displaying the filtered genes.In this table, further manual filtering can be done to assist in discerning whether or the not the candidate gene is likely orthologous and/or has grounds for experimental validation. Depending on the organism, various annotations are provided to help the user determine homology, including KEGG, EC, KOG, PANTHER, PFAM, and FSF. Some of these annotations also have outgoing links to help the user learn more about the properties of the annotation. In addition, annotations that are common between genes are highlighted, as well as sequence statistics such as percent identity and e-value.

ortholog, blastp

OrthoMCL DB

OrthoMCL DB

 

parev11-GUI-Ubuntu-WIP-V3

parev11-GUI-Ubuntu-WIP-V3

 

PASA

Gene Structure Annotation and Analysis Using PASA

PASA

Pegasus Workflow Host v.1

Submit host for Pegasus workflows

pegasus

Pegasus Workflow Host v.2

Host for managing Pegasus workflows

pegasus

Pegasus Workflow Host v.3

A submit host to submit and manage Pegasus workflows

pegasus

Perl Webserver

Perl Webserver

 

PhytoImage (11/04/2011)

This image contains a collection of image analysis tools for plant phenotyping --updated 11/04/2011

R

PLINK v1.07

iPlant Base Image with PLINK software installed for whole genome association analysis. (NOTE: Documentation and example data can be found in the /usr/PLINK-docs directory.)

Ubuntu, gwas, plink

Qiime-1.8

Qiime-1.8 ubuntu 12.04

 

Qiime-1.8 v2

QIIME (canonically pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to studies based on billions of sequences from thousands of samples.

QIIME, Ubuntu

qiime_chauser_v1

Qiime

 

qiime_chauser_v1

qiime_chauser_v1

 

QuickDevTest v1

QuickDevTest v1

 

QuickDevTest v1

QuickDevTest v1

 

QuickDevTest v1

QuickDevTest v1

 

R 3.01 and RStudio 0.98.943

Ubuntu 12.04: R 3.01 and R Studio Servers and Desktop (0.98.943) instance with rPlant and party apps installed

R, Ubuntu, RStudio

RepeatExplorer

RepeatExplorer

 

RI Prod v2

RI Prod v2

 

RNA-seq analysis

RNA-seq analysis

 

RNA-Seq Visualization

An image to accompany the Current Protocols in Bioinformatics chapter about Atmosphere. Installed software: R, bioconductor (R package), IGV.

R, IGV

RNA-Seq Workbench Williams 1.0

Created: June -2014This image is equipped with a variety of tools for RNA-Seq analysis. It is also developer friendly with tools like IDLE, Komodo edit, R Studio, and git

FastQC, fastqscreen, trinity, FastX, star, bowtie2, Cufflinks, Cuffdiff, Cuffmerge, SAMtools, cummeRbund, R, goseq, deseq2, edgeR, RStudio, komodoedit, artemis, IGV, git, wine

RNA-Seq Workbench Williams 1.2

Created: June -2014 This image is equipped with a variety of tools for RNA-Seq analysis. It is also developer friendly with tools like IDLE, Komodo edit, R Studio, and git

FastQC, FastX, trinity, fastqscreen, star, bowtie2, Cufflinks, Cuffmerge, Cuffdiff, cummeRbund, SAMtools, R, goseq, deseq2, edgeR, RStudio, komodoedit, artemis, IGV, git, wine, desktop

RNASeq Analysis tools

RNASeq Analysis tools that contain a suit of tools.

R, edgeR, BLAST, blat, bowtie2, tophat2, trinity, rsem

RNASeq Analysis v1

Contains everything needed to take fastq rnaseq reads, map, and find DE genes

R

RNASeq RaviP v5

RNASeq RaviP v5

 

RNASeq_Analysis_gt_V2

Bowtie, R, edgeR, python2.7, pip, samtools, TopHat, BWA, HTSeq, pysam

edgeR, R, Bowtie, SAMtools, RNASeq, Tophat, bwa, HTSeq, pysam, Python2.7

roncrump R INLA Ubuntu NoGUI

roncrump R INLA Ubuntu NoGUI

 

RRVARC_Base

This image contains statistical and bioinformatics software and is intended to help insect and plant genetics research. Designed as part of a collaboration between USDA ARS and NDSU.

Ubuntu, R, Tuxedo, trinity, soapdenovo, FastQC, BLAST, price, Celera Assembler, Velvet,  GMAP,GSNAP, cummeRbund, Cuffdiff, Cuffmerge, Cufflinks, Bowtie

scikit-learn 0.15.1

scikit-learn 0.15.1

 

sheauc Centos 6.5

iRODS/iCAT-enabled server with NETCDF-enabled Pydap server build - under /home/sheauc/PydapTomcat6 - /usr/share/tomcat6 had ERDDAP servlet

 

Sheldon Training Image 07/25/2012

Sheldon Training Image 07/25/2012

 

stacks

A suite of tools to perform NGS analysis

NGS

Tassel -atwyford123

Tassel 3.0 standalone, and fastStructure.

 

TCW v1.3

Transcriptome Computational Workbench is a full-featured graphical tool for annotating, analyzing and comparing transcript and/or peptide sequence datasets. For full information see http://www.agcol.arizona.edu/software/tcw. Start with a "tiny1" instance size to explore the demo projects.

 

Test JMatt v0.1

This is a test image based on iPlant Centos 6.5 NoGUI Base3(2436bf2f-13a7-4118-a349-d3529f79ae16).

 

TNRastic v1_0_1 06/19/2012

TNRastic v1_0_1 06/19/2012

 

TNRS v4

TNRS v4

 

TNRS-Batch-v1

TNRS-Batch-v1

 

   

TSW Workshop Williams 1.0

TSW Workshop Williams 1.0

 

Tuxedo Workbench2

Tuxedo Workbench2

 

uBiomeSeqAnal-psi9533-v2

This image contains IMSAv2 (integrated metagenomic sequence analysis) for creating a pipeline to identify and classify reads originating from the host microbiome.

Bowtie, Ubuntu, BLAST, blat, Metagenomics

Ubuntu 12 - iPlant Base 2014

Ubuntu 12 - iPlant Base 2014

 

Ubuntu 12.04 + Biolinux

4b22c7b1-ae58-410f-b435-79686f4b18a6

 

Ubuntu 12.04 - Base Image 2014

Ubuntu 12.04 - Base Image 2014

 

Ubuntu 12.04 No-GUI

f8fcb023-9f30-48e8-be20-7931ba2a1051

 

Ubuntu 12.04 R and RStudio

Ubuntu 12.04: R and R Studio instance with rPlant and party apps installed

 

Ubuntu 12.04 Unity GUI v1

emi-6A1E30D5

 

Ubuntu 12.04 Updated NoGUI v1

Ubuntu 12.04 Updated NoGUI v1

 

Ubuntu 12.04 Xfce GUI v2

emi-E7F8300F

 

Ubuntu 12.04.5 - iPlant Base

Ubuntu 12.04.5 - iPlant Base

Featured

Ubuntu 12.04: Biolinux Package

25b479c7-2789-4c2f-8d72-87ed80c87899

 

Ubuntu 12.04: R and RStudio

a770412c-1c05-48ae-bcab-d699da2edc82

 

Ubuntu 13.04 NoGUI Base

Ubuntu 13.04 NoGUI Base

 

Ubuntu 13.04 w/Docker

Ubuntu 13.04 w/Docker

 

Ubuntu 13.04 w/Docker 0.9

Ubuntu 13.04 w/Docker 0.9

 

Ubuntu 13.04 XFCE GUI Base

Ubuntu 13.04 XFCE GUI Base

 

ubuntu-14.04-server-cloudimg-amd64-disk1.img

ubuntu-14.04-server-cloudimg-amd64-disk1.img

 

Ubuntu-Python-pylab-version3.1

This has circadian period analysis software install Spectrum resampling, installed in usr/local/

Python2.7, Matlab

Ubuntu-Python-pylab-version3.2

Ubuntu-Python-pylab-version3.2

 

Ubuntu.12.04.boosted

Ubuntu.12.04.boosted

 

Validate-Py v1

Known-truth testing for genome-wide association tools. This program is an updated, Python-compatible version of the original Validate program found in the Discovery Environment and the ValidateToolkit-0.3 Atmosphere instance. Example data for testing is also included.

Python2.7, gwas, python, validate

Validate.py 1-1

Validate 1.1 validate.py

Ubuntu, validate, numpy, pandas, scipy

ValidateToolkit-dalanders-0.3

Includes two command-line tools using R and Python: Simulate and Validate. Simulate and Validate are part of a workflow/pipeline to be able to test GWAS models and software packages using known-truth simulated datasets.

 

Vizualization

Vizualization

 

washjake Agalma V.2

washjake Agalma V.2

 

williams BioClassRoom v2.3 test

williams BioClassRoom v2.3 test

 

xGDBvm-beta

xGDBvm-beta, version 0.90 21-October-2013Virtual server for annotating eukaryotic genomes.

 

xGDBvm-beta1 (vdeleted 2014-02-10)

xGDBvm-beta1

 

xGDBvm-beta2 (vdeleted 2014-02-10)

Virtual server for annotating eukaryotic genomes (beta version). This version has updated architecture to improve performance with mounted devices. Rev 604 (svn)

 

xGDBvm-beta v1.0 (10-Apr-2014)

xGDBvm-beta v1.0 (10-Apr-2014)

 

xGDBvm-beta v1.01 (27-May-14)

Virtual server for annotating eukaryotic genomes (beta version)

 

xGDBvm-beta v1.02 (23-June-14)

Virtual server for annotating eukaryotic genomes (beta version)

 

xGDBvm-beta v1.03 (25-July-14)

Virtual server for annotating eukaryotic genomes (beta version 1.03)

 

xGDBvm-beta v1.04 (25-July-14)

Virtual server for annotating eukaryotic genomes (beta version 1.04)

 

xGDBvm-beta-2 edwins

xGDBvm-beta-2 edwins

 

xGDBvm-dev-AEGeAn

Development image with add track and compare track features, using Daniel Standage's AEGeAn tookit.

 

xGDBvm-gamma5b (vdeleted 2014-02-10)

emi-896B2634