From 5a9f2c1cbdcac4dc992a8a71b9b380da0676d5cc Mon Sep 17 00:00:00 2001 From: Jeremy Miller Date: Sun, 17 Nov 2024 09:17:46 -0800 Subject: [PATCH] Update README.md --- README.md | 28 +++++++--------------------- 1 file changed, 7 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 31d4a46..48e7593 100644 --- a/README.md +++ b/README.md @@ -8,34 +8,20 @@ You can find a detail description of all scrattch.mapping functions here: ![Docu Update notes are here: ![Versions](https://github.com/AllenInstitute/scrattch-mapping/blob/dev_njj/VERSIONS.md) -## Docker - -We have setup a docker environemnt for scrattch.taxonomy and scrattch.mapping that contains all the required dependencies and the current version of all scrattch packages. This docker is accessible through docker hub via: `njjai/scrattch_mapping:0.6.6`. - -#### HPC usage: - -##### Non-interactive -`singularity exec --cleanenv docker://njjai/scrattch_mapping:0.6.6 Rscript YOUR_CODE.R` - -##### Interactive -`singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.6` - - ## Installation -While we advice using the provided docker, you can also install scrattch.mapping directly from github as follows: +### Using docker (recommended) +We have setup a docker environment for scrattch.taxonomy, scrattch.mapping, and scrattch.patchseq that contains all the required dependencies and the current version of all scrattch packages. **See [the readme](https://github.com/AllenInstitute/scrattch/blob/master/README.md#using-docker) for [the parent scrattch package](https://github.com/AllenInstitute/scrattch) for the most up-to-date docker information.** -*Note: slight edits to installation will be needed while repo is private. Also note that `doMC` may need to be installed manually from the download at https://r-forge.r-project.org/R/?group_id=947 if you use Windows.* +### Directly from GitHub (strongly discouraged) -``` -# Quickly, but without the vignettes: -devtools::install_github("AllenInstitute/scrattch-mapping") +While we advise using the provided docker, you can also install scrattch.mapping directly from GitHub as follows: -# More slowly, but with the vignettes: -devtools::install_github("AllenInstitute/scrattch-mapping",build_vignettes=TRUE, force=TRUE) +``` +devtools::install_github("AllenInstitute/scrattch.mapping") ``` -Note that this strategy might not work outside the docker due to complicated dependencies. Vignettes are provided below. +This strategy **might not work** due to complicated dependencies. Also note that `doMC` may need to be installed manually from [HERE](https://r-forge.r-project.org/R/?group_id=947) if you use Windows. Vignettes are provided below. ## Usage examples