marcjwilliams1/dnds-clonesize-container:latest
$ singularity pull shub://marcjwilliams1/dnds-clonesize-container:latest
Singularity Recipe
Bootstrap: docker
From: jupyter/datascience-notebook
# add R packages from CRAN
Rscript -e "install.packages(pkgs = c('devtools', 'ggplot2', 'dplyr', 'tidyr', 'stringr', 'cowplot', 'gtools', 'argparse','jcolors', 'ggthemes', 'viridis', 'forcats', 'Hmisc', 'readr', 'ggridges', 'readxl', 'purrr', 'bayestestR'), \
repos='https://cran.revolutionanalytics.com/', \
dependencies=TRUE, \
clean = TRUE)"
#add R packages from bioconductor
Rscript -e "install.packages('BiocManager')"
Rscript -e "library(BiocManager); install('GenomicRanges')"
Rscript -e "library(BiocManager); install('IRanges')"
Rscript -e "library(BiocManager); install('Biostrings')"
Rscript -e "library(BiocManager); install('Rsamtools')"
Rscript -e "library(BiocManager); install('seqinr')"
Rscript -e "library(BiocManager); install('rtracklayer')"
Rscript -e "library(BiocManager); install('TCGAbiolinks')"
# add R packages from github
Rscript -e "library(devtools); install_github('im3sanger/dndscv')"
#add julia packages
julia -e "import Pkg; Pkg.add(\"Distributions\")"
julia -e "import Pkg; Pkg.add(\"DataFrames\")"
julia -e "import Pkg; Pkg.add(\"Optim\")"
julia -e "import Pkg; Pkg.add(\"ArgParse\")"
julia -e "import Pkg; Pkg.add(\"Distances\")"
julia -e "import Pkg; Pkg.add(\"CSV\")"
julia -e "import Pkg; Pkg.add(\"Plots\")"
julia -e "import Pkg; Pkg.add(\"Flux\")"
julia -e "import Pkg; Pkg.add(\"Revise\")"
julia -e "import Pkg; Pkg.add(\"StatsBase\")"
julia -e "import Pkg; Pkg.add(\"LinearAlgebra\")"
julia -e "import Pkg; Pkg.add(\"ProgressMeter\")"
julia -e "import Pkg; Pkg.add(\"NLSolversBase\")"
julia -e "import Pkg; Pkg.add(\"RCall\")
Collection
- Name: marcjwilliams1/dnds-clonesize-container
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/marcjwilliams1-dnds-clonesize-container-latest |
collection name | marcjwilliams1/dnds-clonesize-container |
branch | master |
tag | latest |
commit | 510900b47009b71818eb479e2bb55a63f657ad17 |
version (container hash) | 1e97c691d6df7e7a1e0d49012e12fd27 |
build date | 2019-10-24T14:11:14.306Z |
size (MB) | 5015.0 |
size (bytes) | 1814319135 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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