From ef0313765ccf3137d0daeec1274011866a8d76c3 Mon Sep 17 00:00:00 2001 From: Christopher Harrison Date: Thu, 8 Feb 2024 14:11:21 +0000 Subject: [PATCH] Made bin script more explicit in setup Also: * Linked to documentation RE bundling executables * Moved chmod instructions up as subsection, to keep things together --- docs/hands_on/03_setup.md | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/docs/hands_on/03_setup.md b/docs/hands_on/03_setup.md index 5bac65f6..2dd9ca32 100644 --- a/docs/hands_on/03_setup.md +++ b/docs/hands_on/03_setup.md @@ -12,16 +12,17 @@ In the gitpod window, you'll see a terminal. Type the following command to switc cd /workspace/gitpod/hands-on ``` -## Pipeline data +## Pipeline data and scripts -All the files needed for the hands-on activity are stored in the directory shown below: +All the files needed for the hands-on activity are stored in the directory shown below. +This includes all input data (in the `data` directory) and the scripts +required by the workflow (in the `bin` directory; see [documentation](https://nextflow.io/docs/latest/sharing.html#bundling-executables-in-the-workflow)). ```bash tree /workspace/gitpod/hands-on ``` ```bash -/workspace/gitpod/hands-on hands-on ├── README.md ├── bin @@ -45,9 +46,17 @@ hands-on │   └── ENCSR000CPO2_2.fastq.gz ├── final_main.nf └── nextflow.config -``` 4 directories, 19 files +``` + +### Script permission + +Make sure the following R script has execute permissions: + +```bash +chmod +x /workspace/gitpod/hands-on/bin/gghist.R +``` ## Pulling the Docker image @@ -85,11 +94,3 @@ root@0c3770b24a24:/# ``` Type `exit` to exit the container and come back to your shell. - -## Script permission - -Make sure the following R script has execute permissions: - -```bash -chmod +x /workspace/gitpod/hands-on/bin/gghist.R -```