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https://github.com/broadinstitute/taigr
Light weight R package for loading datasets from taiga. Conveniently caches data to your hard disk.
https://github.com/broadinstitute/taigr
Last synced: about 2 months ago
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Light weight R package for loading datasets from taiga. Conveniently caches data to your hard disk.
- Host: GitHub
- URL: https://github.com/broadinstitute/taigr
- Owner: broadinstitute
- Created: 2019-09-23T17:18:57.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-03-05T04:27:07.000Z (7 months ago)
- Last Synced: 2024-07-13T00:30:13.195Z (2 months ago)
- Language: R
- Size: 61.5 KB
- Stars: 0
- Watchers: 19
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- AwesomeGenomics - taigaR
README
# taigr
Light weight R package for loading datasets from taiga. Conveniently caches data to your hard disk.
The latest version of this library is a thin wrapper around `taigaclient` which is part of [taigapy](https://github.org/broadinstitute/taigapy). As a result the first step is to install taigapy into a python environment.
Prerequistes:
1. conda: You can download miniconda from https://docs.anaconda.com/free/miniconda/miniconda-install/ and the instructions below will use the `conda` command to set up the python environment in which we'll install taigapy.
2. git: Can be downloaded from https://git-scm.com/downloads and is used by some of the steps below to pull code from github.
3. The R devtools package: Can be installed via `install.packages('devtools')`
## Installation
### 1. Create a python environment and installing taigapy into it:
```
conda create -n taigapy python=3.9
conda activate taigapy
pip install git+https://github.com/broadinstitute/taigapy.git
```
### 2. Install taigr in an R session
```R
library(devtools)
devtools::install_github("https://github.com/broadinstitute/taigr")
```
### 3. Set up token
You need to get your authorization token so the client library can make requests on your behalf. Go to https://cds.team/taiga/token/ and click on the "Copy" button to copy your token. Paste your token in a file at `~/.taiga/token`. You can do this in R via:
On MacOS:
```R
dir.create(path.expand("~/.taiga"))
write("YOUR_TOKEN_HERE", file=path.expand("~/.taiga/token"))
```
On Windows (write it to two locations to be safest):
```
token <- "YOUR_TOKEN_HERE"
home.dir <- Sys.getenv("USERPROFILE")
dir.create(file.path(home.dir, ".taiga"))
write(token, file=file.path(home.dir, ".taiga", "token"))
home.dir <- Sys.getenv("HOME")
dir.create(file.path(home.dir, ".taiga"))
write(token, file=file.path(home.dir, ".taiga", "token"))
```
### 4. Set up path to taigaclient
`taigr` needs to know where to file the `taigaclient` executable that got installed when `taigapy` was installed. You can tell it by setting the `taigaclient.path` option in R.
In MacOS, this would typically be:
```
options(taigaclient.path=path.expand("~/miniconda3/envs/taigapy/bin/taigaclient"))
```
Or in Windows, this would typically be:
```
options(taigaclient.path=file.path(Sys.getenv("USERPROFILE"), "miniconda3/envs/taigapy/Scripts/taigaclient"))
```
( You may want to put this command in your ".Rprofile" so that it automatically executes each time R starts up as described in https://www.statmethods.net/interface/customizing.html )
At this point taigr should be successfully set up and you can test it out by running:
```
taigr::load.from.taiga("taigr-data-40f2.7/tiny_matrix")
```
( If you get an error like `The following command reported an error...` the first thing to check is whether the command it's reporting failed does actually exist at that location. )
If successful, it should have retreived the 2x3 matrix which was listed at https://cds.team/taiga/dataset/taigr-data-40f2/7
## Installation in a docker container
Similarly, install taigapy and then install taigr from a source bundle to avoid needing to install devtools
```sh
RUN curl -L -o taigr.zip https://github.com/broadinstitute/taigr/archive/master.zip && \
unzip taigr.zip && \
cd taigr-master && \
R CMD INSTALL .
```
## Quick start
```R
library(taigr)
demeter <- load.from.taiga(
data.name = "demeter-2-data-20123df",
data.version = 1)
```
## Package documentation
```R
package?taigr
?load.from.taiga
```
## Development
To test your changes, run the following line in R
```R
devtools::install(pkg=".")
```