Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary
Repository
R client for SODAR
Basic Info
- Host: GitHub
- Owner: bihealth
- License: other
- Language: R
- Default Branch: main
- Size: 17.6 KB
Statistics
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
LimsaR
A simple implementation of the SODAR API to access the SODAR features from R.
Installation
You can install the development version of LimsaR from GitHub with:
``` r
install.packages("devtools")
devtools::install_github("bihealth/LimsaR") ```
Quick start
Authentication
First, you need to know what your SODAR server is. For example, it can be https://sodar-demo.cubi.bihealth.org/.
Second you need to get hold of the API token. Without the token, you will not be able to work with LimsaR.
Once you have the server and the token, say, 'asdfb891823basdfuwerbce', before you start working you need to configure your access.
r
library(LimsaR)
token <- "asdfb891823basdfuwerbce"
sodar_url <- c("https://sodar-demo.cubi.bihealth.org")
sodar_config(token, sodar_url)
If you are a user of cubi-tk,
chances are you have already set up the SODAR configuration in your
~/.cubitkrc.toml file. In that case, you can use the configr package
to load the configuration:
```r library(configr)
access <- read.config("~/.cubitkrc.toml")
sodarconfig(sodarapitoken = access$global$sodarapitoken, sodarurl = access$global$sodarserverurl) ```
Working with SODAR
Now you can get a data frame containing the projects and categories that are visible to you:
r
projects <- sodar_project_list()
Or check exactly who you are:
r
sodar_whoami()
A large part of the SODAR API is implemented. You can create and modify the projects. You can upload and download sample sheets. You can create and manipulate tickets, landing zones and delete requests. For example, if you have a project UUID and the project has a study and iRODS associated, you can create a landing zone with
```r lz <- sodarlzcreate(project_uuid)
gets the UUID of the LZ
lzuuid <- lz$sodaruuid ```
and then check its status, and validate and move it with
r
sodar_lz_status(lz_uuid)
sodar_lz_move(lz_uuid)
Why LimsaR
Limsa is "Soda" in Finnish.
Owner
- Name: Berlin Institute of Health
- Login: bihealth
- Kind: organization
- Website: https://www.cubi.bihealth.org/
- Repositories: 215
- Profile: https://github.com/bihealth
BIH Core Unit Bioinformatics & BIH HPC IT
GitHub Events
Total
- Watch event: 1
- Member event: 1
- Push event: 21
- Create event: 3
Last Year
- Watch event: 1
- Member event: 1
- Push event: 21
- Create event: 3
Dependencies
- colorDF * imports
- dplyr * imports
- httr * imports
- isaeditor >= 0.1.1 imports
- jsonlite * imports