Merge branch 'master' into new_som

Dockerfile

@@ -22,5 +22,5 @@ RUN R -e "install.packages('BiocManager')"
 RUN R -e "BiocManager::install('FlowSOM')"
 RUN R -e "BiocManager::install('ConsensusClusterPlus')"
 
-# jupyter notebook
-CMD ["jupyter", "notebook", "--ip=0.0.0.0", "--allow-root"]
+# jupyter lab
+CMD jupyter lab --ip=0.0.0.0 --allow-root --no-browser --port=$JUPYTER_PORT

README.md

@@ -38,7 +38,7 @@ You've now installed the code base.
 Enter the following command into terminal from the same directory you ran the above commands:
 
 ```
-bash start_docker.sh
+./start_docker.sh
 ``` 
 
 This will generate a link to a jupyter notebook. Copy the last URL (the one with `127.0.0.1:8888` at the beginning) into your web browser.
@@ -47,7 +47,7 @@ Be sure to keep this terminal open.  **Do not exit the terminal or enter control
 
 ### NOTE
 
-If you already have a Jupyter session open when you run `$ bash start_docker.sh`, you will receive a couple additional prompts. 
+If you already have a Jupyter session open when you run `$ ./start_docker.sh`, you will receive a couple additional prompts. 
 
 Copy the URL listed after `Enter this URL instead to access the notebooks:` 
 
@@ -75,11 +75,11 @@ git pull
 
 Then, run the command below to update the jupyter notebooks to the latest version
 ```
-bash start_docker.sh --update
+./start_docker.sh --update
 ```
 or
 ```
-bash start_docker.sh -u
+./start_docker.sh -u
 ```
 
 If the requirements.txt has changed, Docker will rebuild with the new dependencies first.

start_docker.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # if requirements.txt has been changed in the last day, automatically rebuild Docker first
 if [[ $(find . -mmin -1440 -type f -print | grep requirements.txt | wc -l) -eq 1 ]]
@@ -13,20 +13,14 @@ bash update_notebooks.sh "$@"
 # find lowest open port available
 PORT=8888
 
-until [[ $(lsof -i -P -n | grep 127.0.0.1:$PORT | wc -l) -eq 0 ]]
+until [[ $(docker container ls | grep 0.0.0.0:$PORT | wc -l) -eq 0 ]]
   do
-    ((PORT=PORT+1))
+    ((PORT=$PORT+1))
 done
 
-if [ $PORT -ne 8888 ]
-  then
-    echo "WARNING: another Jupyter server on port 8888 running"
-    echo "Enter this URL instead to access the notebooks: http://127.0.0.1:$PORT/"
-    echo "In the URLs below, copy the token after \"token=\", paste that into the password prompt, and log in"
-fi
-
 docker run -it \
-  -p $PORT:8888 \
+  -p $PORT:$PORT \
+  -e JUPYTER_PORT=$PORT\
   -v "$PWD/ark:/usr/local/lib/python3.6/site-packages/ark" \
   -v "$PWD/scripts:/scripts" \
   -v "$PWD/data:/data" \