https://github.com/bcbi/bcbi_base.jl
Julia packages commonly used by the Brown Center for Biomedical Informatics (BCBI)
https://github.com/bcbi/bcbi_base.jl
Last synced: 4 months ago
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Julia packages commonly used by the Brown Center for Biomedical Informatics (BCBI)
- Host: GitHub
- URL: https://github.com/bcbi/bcbi_base.jl
- Owner: bcbi
- License: mit
- Created: 2017-05-10T11:49:31.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2020-02-08T20:32:35.000Z (over 6 years ago)
- Last Synced: 2025-03-27T23:23:41.273Z (over 1 year ago)
- Language: Julia
- Homepage:
- Size: 52.7 KB
- Stars: 1
- Watchers: 6
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: CODEOWNERS
Awesome Lists containing this project
README
# BCBI Metapackage
| Travis CI | Coverage | License |
|-----------|----------|---------|
|[](https://travis-ci.org/bcbi/BCBI_base.jl)|[](http://codecov.io/githubbcbi/BCBI_base.jl?branch=master)|[](https://raw.githubusercontent.com/bcbi/BCBI_base.jl/bcbi_v0.0.0/LICENSE.md)|
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
```julia
Pkg.clone("https://github.com/bcbi/BCBI_base.jl.git")
```
## URSA/STRONGHOLD
See [instructions](https://github.com/bcbi/BCBI_base.jl/blob/master/STRONGHOLD.md)
## General Usage
* Import package
```julia
using BCBI_base
```
* Install all packages
One set at a time
```julia
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
```julia
install_all()
````
* Check that installed packages precompile correctly
It is best to call this from a new/fresh julia session
```julia
using_all()
```
* Remove packages that are not working (recommended)
```julia
BCBI_base.clean_up()
```
* Get list of missing "desired" packages
```julia
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|||||
* To print the list of packages installed by this version:
```julia
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
* The MySQL.jl package depends on a working MySQL installation; instructions can be obtained [here](https://dev.mysql.com/doc/refman/5.7/en/installing.html). For simplicity, macOS users may prefer to install MySQL using [Homebrew](https://brew.sh/).
* The RCall.jl package depends on a working installation of R, which can be obtained [here](https://www.r-project.org/). MacOS users may opt to use [Homebrew](https://brew.sh/) for ease of installation.