BCBI Metapackage
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This package is a collection of Julia packages used by the Brown Center for Biomedical Informatics (BCBI). The package serves as a mechanism for installing the various Julia packages most frequently used at BCBI.
Installation
Pkg.clone("https://github.com/bcbi/BCBI_base.jl.git")URSA/STRONGHOLD
See instructions
General Usage
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Import package
using BCBI_base -
Install all packages
One set at a time
BCBI_base.add(BCBI_base.base_pkgs) BCBI_base.add(BCBI_base.plotting_pkgs) BCBI_base.add(BCBI_base.datasets_pkg) BCBI_base.add(BCBI_base.external_pkgs) BCBI_base.clone(BCBI_base.clone_pkgs) BCBI_base.checkout(BCBI_base.checkout_pkgs)Alternatively, if you are confident things won't fail
install_all() -
Check that installed packages precompile correctly
It is best to call this from a new/fresh julia session
using_all() -
Remove packages that are not working (recommended)
BCBI_base.clean_up() -
Get list of missing "desired" packages
check_installed()
List of packages
| Base | Plotting | DataSets | R/Python | Cloned |
|---|---|---|---|---|
| MySQL | PGFPlotsX | RDataSets | RCall | ARules=>https://github.com/bcbi/ARules.jl |
| BioServices | PlotlyJS | VegaDatasets | PyCall | ScikitLearn=>https://github.com/cstjean/ScikitLearn.jl.git |
| ClassImbalance | Pandas | Gadfly=>https://github.com/GiovineItalia/Gadfly.jl.git | ||
| Clustering | Pandas | BioMedQuery=>https://github.com/bcbi/BioMedQuery.jl.git | ||
| Compat | Seaborn | Lasso=>https://github.com/simonster/Lasso.jl.git | ||
| CSV | PredictMD=>https://github.com/bcbi/PredictMD.jl | |||
| DataFrames | ||||
| DecisionTree | ||||
| EzXML | ||||
| GLM | ||||
| GLMNet | ||||
| HTTP | ||||
| HypothesisTests | ||||
| IJulia | ||||
| JLD | ||||
| JLD2 | ||||
| JuliaDB | ||||
| Lasso | ||||
| LIBSVM | ||||
| LightXML | ||||
| MixedModels | ||||
| Revise | ||||
| ROCAnalysis | ||||
| StatsBase | ||||
| Query |
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To print the list of packages installed by this version:
using BCBI_base println(BCBI_base.base_pkgs) println(BCBI_base.plotting_pkgs) println(BCBI_base.external_pkgs) println(BCBI_base.datasets_pkgs) println(BCBI_base.clone_pkgs) println(BCBI_base.checkout_pkgs)
Other Dependencies
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The MySQL.jl package depends on a working MySQL installation; instructions can be obtained here. For simplicity, macOS users may prefer to install MySQL using Homebrew.
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The RCall.jl package depends on a working installation of R, which can be obtained here. MacOS users may opt to use Homebrew for ease of installation.