From f6e2d0093c2836c1a7eb222fd301c41e9b87df97 Mon Sep 17 00:00:00 2001 From: Bai juyi Date: Tue, 4 Jun 2024 12:13:12 +0200 Subject: [PATCH] readme update about quick deployment --- readme.md | 41 +++++++++++++++++++++++++++-------------- 1 file changed, 27 insertions(+), 14 deletions(-) diff --git a/readme.md b/readme.md index f0e52af..003292d 100644 --- a/readme.md +++ b/readme.md @@ -8,7 +8,7 @@ This is a Shiny app developed for PMET. ```shell . -├── conf * # configure for shiny server and nginx +├── conf * # configure for shiny server and nginx ├── data ├── dockerfiles ├── PMETdev @@ -22,43 +22,57 @@ This is a Shiny app developed for PMET. │ └── utils ├── result ├── www -├── 01_deploy_via_bash.sh -├── 01_deploy_via_Docker.sh * # Recommended installation method -├── app.R * # Shiny app +├── 01_deploy_via_Docker.sh +├── 01_deploy_via_singularity.sh * # Recommended installation method +├── app.R * # Shiny app ├── docker-compose.yml ├── PMET-Shiny-App.Rproj └── readme.md ``` ## 2. Quick deployment + ### 2.1 (option one) Install on Docker (Recommended) ```bash -bash 01_deploy_via_Docker.sh +bash 01_deploy_via_singularity.sh ``` ### 2.2 (option two) Bash install on current Debian-like OS +```bash +bash 01_deploy_via_Docker.sh +``` + +### 2.3 (discarded) Bash install on current Debian-like OS + 1. Install `Shiny Server` and `Nginx` [[details](#setup-shiny-server-and-nginx)] + 2. `git clone` in the folder of Shiny Server (default: `/srv/shiny-server`) or git clone anywhere and then create a link under `/srv/shiny-server` as shown below: -![](https://raw.githubusercontent.com/duocang/images/master/PicGo/202309191728114.png) + ![](https://raw.githubusercontent.com/duocang/images/master/PicGo/202309191728114.png) -1. Run `01_deploy_via_bash.sh` +3. Run `01_deploy_via_bash.sh` + + ``` + bash archive/01_deploy_via_bash.sh + ``` - 1. set email and CPU + - 2. assign execute permissions + - 3. download data of homotypic motif hits of 21 speices [[details](#index-data)] + - 4. compile binaries needed by Shiny app [[details](#compile)] + - 5. install R packages + - 6. install python packages - - 7. Install tools (`GNU Parallel`, `bedtools`, `samtools`, `MEME`...)[[details](#tools)] - ```bash - bash 01_deploy_via_bash.sh - ``` - ![](https://raw.githubusercontent.com/duocang/images/master/PicGo/202310190148145.png) + - 7. Install tools (`GNU Parallel`, `bedtools`, `samtools`, `MEME`...)[[details](#tools)] + ![](https://raw.githubusercontent.com/duocang/images/master/PicGo/202310190148145.png) --- @@ -66,7 +80,6 @@ bash 01_deploy_via_Docker.sh --- - ## 3. Pre-computed homotypic motif hits of plant species (PMET indexing data) Given that the PMET indexing calculation takes a very long time, we have already performed pre-calculation for some plants and several common plant transcription factor databases. @@ -162,8 +175,8 @@ server { } ``` - ## PMET workflow + ![](www/figures/pmet_workflow_with_interval_option.png) [GitHub Ribbons](https://github.blog/2008-12-19-github-ribbons/)