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‎Dockerfile‎

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FROM arcolombo/arkasgithublayer:v1
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COPY /runScripts /bin
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COPY /arkasAnalysisBaseSpace /arkasAnalysisBaseSpace
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COPY /arkasBasespace /arkasBasespace
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COPY /outputReport /outputReport
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COPY /Rccdashboard /Rccdashboard
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RUN R CMD INSTALL /Rccdashboard
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RUN R CMD INSTALL /arkasAnalysisBaseSpace
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RUN R CMD INSTALL /arkasBasespace
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COPY /speedSage_1.03.tar.gz /speedSage_1.03.tar.gz
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RUN R -e 'library(BiocInstaller);biocLite(c("Rcpp","RcppArmadillo","biomaRt"),ask=FALSE)'
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RUN R CMD INSTALL /speedSage_1.03.tar.gz

‎Dockerfile~‎

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FROM arcolombo/arkasgithublayer:v1
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COPY /runScripts /bin
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COPY /arkasAnalysisBaseSpace /arkasAnalysisBaseSpace
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COPY /arkasBasespace /arkasBasespace
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COPY /outputReport /outputReport
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COPY /Rccdashboard /Rccdashboard
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RUN R CMD INSTALL /Rccdashboard
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RUN R CMD INSTALL /arkasAnalysisBaseSpace
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RUN R CMD INSTALL /arkasBasespace
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COPY /speedSage_1.03.tar.gz /speedSage_1.03.tar.gz
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RUN R -e 'library(BiocInstaller);biocLite(c("Rcpp","RcppArmadillo"),ask=FALSE)'
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RUN R CMD INSTALL /speedSage_1.03.tar.gz

‎README.md‎

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# Arkas BaseSpace Application
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the arkasBasespace library parses the single node json, handling multi-custom fasta upload appresults, multi control appResults, and multi comparisons appResults.
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#arkasBasespace
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arkasBasespace in the analysis function will contain more scripts not related to quantifying on the cloud , but analyzing on the cloud, this arkasBasespace R package is a superset, and should be the final R package for cloud computing.
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#Docker Container
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this Dockerfile currently builds arcolombo/arkasanalysis:v2 FROM arcolombo/arkasgithublayer:v1
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#steps for revising this package.
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If you need to revise parts of the package, edit the libraries in this directory and rebuild arcolombo/arkasanalysisbasespace:v1. this builds ontop of githublayers. so you don't need to re-install R packages or enviroment package dependencies. only need to edit and re-install the last layer specific to arkas.
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#updating the transcriptomes needs documentation
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add steps on maintaining here.

‎RLibraries/EnsDbLite.Hsapiens.84/DESCRIPTION‎

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Package: EnsDbLite.Hsapiens.84
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Title: Ensembl-based annotation package
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Description: Lightweight Ensembl transcript annotations
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Version: 1.0
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Author: .
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Maintainer: .<[email protected]>
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Depends: TxDbLite
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Imports: GenomicFeatures, RSQLite
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License: Artistic-2.0
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organism: Homo sapiens
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species: Homo sapiens
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provider: Ensembl
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provider_version: GRCh38
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release_date: Tue Apr 12 13:53:44 2016
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resource_url: ftp://ftp.ensembl.org/pub/release-GRCh38
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biocViews: AnnotationData, EnsDbLite, Homo_sapiens

‎RLibraries/EnsDbLite.Hsapiens.84/NAMESPACE‎

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##import(AnnotationDbi)
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import(GenomicFeatures)
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import(ensembldb)
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### Don't export EnsDbLite.Hsapiens.84 (the object defined in this
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### package): it is created and dynamically exported at load time (refer
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### to R/zzz.R for the details).
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‎RLibraries/EnsDbLite.Hsapiens.84/R/zzz.R‎

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###
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### Load any db objects whenever the package is loaded.
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###
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.onLoad <- function(libname, pkgname)
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{
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ns <- asNamespace(pkgname)
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path <- system.file("extdata", package=pkgname, lib.loc=libname)
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files <- dir(path)
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for(i in seq_len(length(files))){
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# db <- EnsDbLite(system.file("extdata", files[[i]], package=pkgname,
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# lib.loc=libname))
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db<-EnsDbLite(files[[i]],path)
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objname <- sub(".sqlite$","",files[[i]])
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assign(objname, db, envir=ns)
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namespaceExport(ns, objname)
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}
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}

‎RLibraries/EnsDbLite.Hsapiens.84/inst/extdata/EnsDbLite.Hsapiens.84.sqlite‎

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‎RLibraries/EnsDbLite.Hsapiens.84/man/package.Rd‎

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\name{EnsDbLite.Hsapiens.84}
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\docType{package}
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\alias{EnsDbLite.Hsapiens.84-package}
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\alias{EnsDbLite.Hsapiens.84}
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\alias{EnsDbLite.Hsapiens.84}
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\title{Ensembl-based annotation package}
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\description{
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This package loads an SQL connection to a database containing
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annotations from Ensembl. For examples and help on functions see the
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help pages from the \code{ensembldb} package!
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}
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\note{
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This data package was made from resources at Ensembl on
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Tue Apr 12 13:53:44 2016 and based on the GRCh38
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}
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\author{.}
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\examples{
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## load the library
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##library(EnsDbLite.Hsapiens.84)
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## list the contents that are loaded into memory
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ls('package:EnsDbLite.Hsapiens.84')
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## show the db object that is loaded by calling it's name
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EnsDbLite.Hsapiens.84
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## for more examples see the ensembldb package.
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}
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\keyword{package}
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\keyword{data}

‎RLibraries/EnsDbLite.Mmusculus.84/DESCRIPTION‎

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Package: EnsDbLite.Mmusculus.84
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Title: Ensembl-based annotation package
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Description: Lightweight Ensembl transcript annotations
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Version: 1.0
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Author: .
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Maintainer: .<[email protected]>
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Depends: TxDbLite
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Imports: GenomicFeatures, RSQLite
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License: Artistic-2.0
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organism: Mus musculus
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species: Mus musculus
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provider: Ensembl
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provider_version: GRCm38
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release_date: Wed Apr 20 15:33:50 2016
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resource_url: ftp://ftp.ensembl.org/pub/release-GRCm38
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biocViews: AnnotationData, EnsDbLite, Mus_musculus

‎RLibraries/EnsDbLite.Mmusculus.84/NAMESPACE‎

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##import(AnnotationDbi)
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import(GenomicFeatures)
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import(ensembldb)
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### Don't export EnsDbLite.Mmusculus.84 (the object defined in this
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### package): it is created and dynamically exported at load time (refer
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### to R/zzz.R for the details).
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