initial commit

README.md

@@ -1,3 +1,3 @@
-# NeSI training environment ML102 Jupyter app
+# NeSI training environment Intermediate Shell for Bioinformatics app
 
-JupyterLab app for running the ML102 workshop on the NeSI training environment.
+JupyterLab app for running Intermediate Shell for Bioinformatics on the NeSI training environment.

docker/Dockerfile

@@ -3,6 +3,7 @@ FROM ubuntu:22.04
 # install system dependencies
 # TODO: move ldap-utils, libnss-ldapd, libpam-ldapd, nscd, nslcd to base image??
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        bioawk \
         curl \
         git \
         ldap-utils \
@@ -23,25 +24,16 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
         zip \
     && rm -rf /var/lib/apt/lists/*
 
-# download the required image files into the container image
-RUN wget -nv https://storage.googleapis.com/download.tensorflow.org/example_images/flower_photos.tgz \
-        -O /var/lib/flower_photos.tgz \
-    && tar -xzf /var/lib/flower_photos.tgz -C /var/lib \
-    && rm -f /var/lib/flower_photos.tgz \
-    && chown -R root:root /var/lib/flower_photos \
-    && chmod -R o+rX /var/lib/flower_photos \
-    && wget -nv https://storage.googleapis.com/mledu-datasets/cats_and_dogs_filtered.zip \
-        -O /var/lib/cats_and_dogs_filtered.zip \
-    && unzip -q -d /var/lib /var/lib/cats_and_dogs_filtered.zip \
-    && rm -f /var/lib/cats_and_dogs_filtered.zip \
-    && chown -R root:root /var/lib/cats_and_dogs_filtered \
-    && chmod -R o+rX /var/lib/cats_and_dogs_filtered
-
-# copy the repo source (e.g. notebooks) to the container image and install dependencies
-ARG ML102_HASH="39f654a10ddcfaa06420c12173f6053ea9963d26"
-RUN git clone https://github.com/nesi/ml102_workshop.git /opt/ml102_workshop \
-    && cd /opt/ml102_workshop \
-    && git checkout $ML102_HASH \
-    && pip3 --no-cache-dir install -r requirements.txt \
-    && pip3 --no-cache-dir install jupyterlab \
-    && rm -rf /opt/ml102_workshop/.git
+# download the required data into the container image and make sure permission are ok
+RUN wget -nv https://github.com/GenomicsAotearoa/shell-for-bioinformatics/releases/download/v2.0/puzzles_da.tar.gz \
+        -O /var/lib/puzzles_da.tar.gz \
+    && tar -xzf /var/lib/puzzles_da.tar.gz -C /var/lib \
+    && rm -f /var/lib/puzzles_da.tar.gz \
+    && chown -R root:root /var/lib/puzzles_da \
+    && chmod -R o+rX /var/lib/puzzles_da \
+    && wget -nv https://github.com/GenomicsAotearoa/shell-for-bioinformatics/releases/download/v2.0/shell4b_data.tar.gz \
+        -O /var/lib/shell4b_data.tar.gz \
+    && tar -xzf /var/lib/shell4b_data.tar.gz -C /var/lib \
+    && rm -f /var/lib/shell4b_data.tar.gz \
+    && chown -R root:root /var/lib/shell4b_data \
+    && chmod -R o+rX /var/lib/shell4b_data

manifest.yml

@@ -1,7 +1,7 @@
 ---
-name: ML102
+name: Intermediate shell for bioinformatics
 category: Interactive Apps
 subcategory: Servers
 role: batch_connect
 description: |
-  This app will launch a Jupyter Lab server for the ML102 workshop
+  This app will launch a Jupyter Lab server for the intermediate shell for bioinformatics workshop

submit.yml.erb

@@ -16,8 +16,8 @@ script:
   wall_time: "<%= wall_time.to_i * 3600 %>"
   native:
     container:
-      name: "ml102"
-      image: "ghcr.io/nesi/training-environment-jupyter-ml102-app:v0.2.0"
+      name: "intermshell"
+      image: "ghcr.io/nesi/training-environment-jupyter-intermediate-shell-app:v0.1.0"
       command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"]
       working_dir: "<%= Etc.getpwnam(ENV['USER']).dir %>"
       restart_policy: 'OnFailure'
@@ -56,7 +56,7 @@ script:
             c.ServerApp.port_retries = 0
             c.ServerApp.open_browser = False
             c.ServerApp.allow_origin = '*'
-            c.ServerApp.root_dir = '<%= user.home %>/ml102_workshop'
+            c.ServerApp.root_dir = '<%= user.home %>/shell4b'
             c.ServerApp.disable_check_xsrf = True
           mount_path: '/ood'
     init_containers:

template/script.sh.erb

@@ -1,23 +1,26 @@
 #!/usr/bin/env bash
 
+# send all output to pod.log
 exec &> >(tee -a "${LOG_DIR}/pod.log")
 
-# Benchmark info
 echo "TIMING - Starting main script at: $(date)"
 
+# copying config file for debugging
 cp /ood/ondemand_config.py ./
 
 # Set working directory to home directory
 cd "${HOME}"
 
-#
-# Start Jupyter Notebook Server
-#
-
-# Benchmark info
 echo "TIMING - Starting jupyter at: $(date)"
 
-# Launch the Jupyter Notebook Server
 set -x
-rsync --ignore-existing -avz /opt/ml102_workshop/ ~/ml102_workshop/
+
+# copy data files
+# note: this will not overwrite files if they already exist, so changes won't
+#       be lost when restarting the app
+mkdir -p ~/shell4b
+rsync --ignore-existing -avz /var/lib/puzzles_da/ ~/shell4b/puzzles_da/
+rsync --ignore-existing -avz /var/lib/shell4b_data/ ~/shell4b/shell4b_data/
+
+# launch JupyterLab
 jupyter lab --config="/ood/ondemand_config.py"

view.html.erb

@@ -1,7 +1,7 @@
 <form action="/node/<%= host %>/<%= port %>/login" method="post" target="_blank">
   <input type="hidden" name="password" value="<%= password %>">
   <button class="btn btn-primary" type="submit">
-    <i class="fa fa-registered"></i> Connect to ML102 JupyterLab
+    <i class="fa fa-registered"></i> Connect to Intermediate Shell app
   </button>
 </form>