Sync develop with main (#9)

.github/workflows/publish.yml

@@ -21,6 +21,8 @@ env:
 jobs:
 
   publish:
+    # Only run this action in the forked development repository
+    if: github.repository == 'alfredeen/Gene_Catalog_Rshiny'
 
     runs-on: ubuntu-latest
     permissions:

Dockerfile

@@ -3,7 +3,6 @@ FROM rocker/shiny:latest
 #  "shiny"
 
 ENV USER=shiny
-#RUN useradd -m -u 1000 $USER
 
 # Install system dependencies including those for tidyverse
 RUN apt-get update && \
@@ -35,8 +34,8 @@ RUN R -e "install.packages('remotes')" \
     && R -e "remotes::install_version('tidyverse', version = '2.0.0', dependencies= T)" \
     && R -e "remotes::install_version('arrow', version = '14.0.0', dependencies= T)" \
     && R -e "remotes::install_version('data.table', version = '1.14.8', dependencies= T)" \
-    #&& R -e "remotes::install_version('rBLAST', repos = 'https://mhahsler.r-universe.dev', dependencies= T)" \
-    && R -e "remotes::install_github('mhahsler/rBLAST', dependencies= T)" \
+    && R -e "remotes::install_version('rBLAST', repos = 'https://mhahsler.r-universe.dev', dependencies= T, version='0.99.4')" \
+    #&& R -e "remotes::install_github('mhahsler/rBLAST', dependencies= T)" \
     && R -e "remotes::install_version('leaflet', version = '2.1.2', dependencies= T)" \
     && R -e "remotes::install_version('sp', version = '1.6-1', dependencies= T)" \
     && R -e "remotes::install_version('magrittr', version = '2.0.3', dependencies= T)" \
@@ -48,7 +47,7 @@ RUN R -e "install.packages('remotes')" \
     && R -e "remotes::install_version('shinybusy', version = '0.3.1', dependencies= T)"
 
 
-# Custom added
+# Additional packages for logging and diagnosis
 RUN R -e "install.packages('log4r')" \
     && R -e "install.packages('readr')" \
     && R -e "install.packages('RcppTOML')"
@@ -69,7 +68,6 @@ WORKDIR /srv/shiny-server/app
 
 RUN chown -R shiny:shiny . && \
     chmod ug+x start-script.sh
-# end custom modified
 
 
 USER $USER

Dockerfile.ci

@@ -3,7 +3,6 @@ FROM rocker/shiny:latest
 #  "shiny"
 
 ENV USER=shiny
-#RUN useradd -m -u 1000 $USER
 
 # Install system dependencies including those for tidyverse
 RUN apt-get update && \
@@ -48,7 +47,7 @@ RUN R -e "install.packages('remotes')" \
     && R -e "remotes::install_version('shinybusy', version = '0.3.1', dependencies= T)"
 
 
-# Custom added
+# Additional packages for logging and diagnosis
 RUN R -e "install.packages('log4r')" \
     && R -e "install.packages('readr')" \
     && R -e "install.packages('RcppTOML')"
@@ -69,7 +68,6 @@ WORKDIR /srv/shiny-server/app
 
 RUN chown -R shiny:shiny . && \
     chmod ug+x start-script.sh
-# end custom modified
 
 
 USER $USER

README.md

@@ -1,26 +1,41 @@
 # Gene_Catalog_Rshiny
-Fork of lfdelzam/Gene_Catalog_Rshiny
 
-For testing variations of building and deploying this Shiny app.
+BAltic Gene Set - BAGS.v1.1
 
-## Development
+## Deploying to the Serve plattform
 
-If planning to run in local environment from R terminal:
-Copy and edit the .Renviron file
+### Configuration
 
-    cp ./.Renviron.template ./app/.Renviron
+The application is configured in the .Renviron.template file. This is initially configured for deployment to the Serve plattform.
 
-If using a local data directory, create the directory and copy a data file there named existing.csv:
+### Setup
 
-    mkdir data
+Upload the dataset to Serve and extract such that the contents reside directly under project-vol. The project-vol directory will be mapped to /data in the container.
+
+Create as custom app type in Serve with the following values:
+
+- Persistent Volume: project-vol
+- Path: /data
+- Port: 3838
+- Image: specify the path to the published image
+- User ID: 999
+
+
+### Viewing logs
+
+    cat /rlogs/app.log
+
+    ls /var/log/shiny-server
+
+## Local deployments
 
 ## Build and run a docker image locally
 
 Configure for the local environment in the .Renviron.template file
 
     R_LOGLEVEL = "DEBUG"
-    R_LOGFILE = "/rlogs/app.log"
-    DATA_DIR = "/data"
+    R_LOGFILE = "../rlogs/app.log"
+    DATA_DIR = "../data"
 
 Build the docker image
 
@@ -32,15 +47,23 @@ Run the container without data folder
 
 Or, run the container with a mounted local data folder
 
+    APP_PATH="PATH-TO-GIT-REPO/Gene_Catalog_Rshiny"
+
     docker run -p 127.0.0.1:3838:3838 \
-    -v $HOME/git/alfredeen/Gene_Catalog_Rshiny/data:/data \
+    -v $APP_PATH/data:/data \
     --memory=16g --memory-swap=20g \
     gene-catalog-rshiny:dev
 
 Browse to the app at  http://localhost:3838/
 
-## View the log files
+## Local development
 
-    cat /rlogs/app.log
+If planning to run in local environment from R terminal:
+Copy and edit the .Renviron file
 
-    ls /var/log/shiny-server
+    cp ./.Renviron.template ./app/.Renviron
+
+If using a local data directory, create the directory and copy a data file there named existing.csv.
+This can be used for diagnosing permission problems.
+
+    mkdir data

app/verify-setup.R

@@ -6,7 +6,7 @@ library(log4r)
 library(RcppTOML)
 
 
-# Settings from env vars
+# Settings from env vars with default initial values
 data_dir <- ""
 log_level <- "DEBUG"
 log_file <- "/rlogs/app.log"