adopt CI a bit

Author: bgruening

.github/workflows/single.sh

@@ -1,18 +1,6 @@
 #!/bin/bash
 set -ex
 
-# Change the default docker data directory as /mnt has more space
-sudo mkdir -p /mnt/docker
-
-if [ ! -f /etc/docker/daemon.json ]; then
-    echo '{}' | sudo tee /etc/docker/daemon.json
-fi
-
-sudo jq '."data-root"="/mnt/docker"' /etc/docker/daemon.json > /tmp/docker_daemon.json
-sudo mv /tmp/docker_daemon.json /etc/docker/daemon.json
-
-sudo systemctl daemon-reload && sudo systemctl restart docker
-
 docker --version
 docker info
 
@@ -22,20 +10,44 @@ export GALAXY_USER_EMAIL=admin@example.org
 export GALAXY_USER_PASSWD=password
 export BIOBLEND_GALAXY_API_KEY=fakekey
 export BIOBLEND_GALAXY_URL=http://localhost:8080
+export EPHEMERIS_IMAGE=${EPHEMERIS_IMAGE:-quay.io/biocontainers/ephemeris:0.10.11--pyhdfd78af_0}
+export GALAXY_WAIT_TIMEOUT=${GALAXY_WAIT_TIMEOUT:-600}
+
+SKIP_SFTP=false
+SKIP_DIVE=false
+
+if [[ "${CI:-}" == "true" ]]; then
+    sudo apt-get update -qq
+    #sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
+    sudo apt-get install sshpass --no-install-recommends -y
+else
+    if ! command -v sshpass >/dev/null 2>&1; then
+        echo "sshpass not found; skipping SFTP test."
+        SKIP_SFTP=true
+    fi
+fi
 
-sudo apt-get update -qq
-#sudo apt-get install docker-ce --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
-sudo apt-get install sshpass --no-install-recommends -y
-
-DIVE_VERSION=$(curl -sL "https://api.github.com/repos/wagoodman/dive/releases/latest" | grep '"tag_name":' | sed -E 's/.*"v([^"]+)".*/\1/')
-curl -OL https://github.com/wagoodman/dive/releases/download/v${DIVE_VERSION}/dive_${DIVE_VERSION}_linux_amd64.deb
-sudo apt install ./dive_${DIVE_VERSION}_linux_amd64.deb
-rm ./dive_${DIVE_VERSION}_linux_amd64.deb
+if [[ "${CI:-}" == "true" ]]; then
+    DIVE_VERSION=$(curl -sL "https://api.github.com/repos/wagoodman/dive/releases/latest" | grep '"tag_name":' | sed -E 's/.*"v([^"]+)".*/\1/')
+    curl -OL https://github.com/wagoodman/dive/releases/download/v${DIVE_VERSION}/dive_${DIVE_VERSION}_linux_amd64.deb
+    sudo apt install ./dive_${DIVE_VERSION}_linux_amd64.deb
+    rm ./dive_${DIVE_VERSION}_linux_amd64.deb
+else
+    if ! command -v dive >/dev/null 2>&1; then
+        echo "dive not found; skipping image analysis."
+        SKIP_DIVE=true
+    fi
+fi
 
-pip3 install ephemeris
+galaxy_wait() {
+    docker run --rm --link galaxy:galaxy \
+        "${EPHEMERIS_IMAGE}" galaxy-wait -g http://galaxy --timeout "${1:-$GALAXY_WAIT_TIMEOUT}"
+}
 
 # start building this repo
-sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+if [[ "${CI:-}" == "true" ]]; then
+    sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
+fi
 
 ## define a container size check function, first parameter is the container name, second the max allowed size in MB
 container_size_check () {
@@ -65,7 +77,8 @@ docker buildx build \
     galaxy/
 #container_size_check   quay.io/bgruening/galaxy  1500
 
-mkdir local_folder
+docker rm -f galaxy httpstest || true
+mkdir -p local_folder
 docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
     --name galaxy \
     --privileged=true \
@@ -105,11 +118,11 @@ echo "SLURM and SGE tests have finished."
 
 docker ps
 echo 'Waiting for Galaxy to come up.'
-galaxy_wait_timeout=600
+galaxy_wait_timeout=$GALAXY_WAIT_TIMEOUT
 galaxy_wait_interval=30
 galaxy_wait_end=$((SECONDS + galaxy_wait_timeout))
 while [ $SECONDS -lt $galaxy_wait_end ]; do
-    if galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 30; then
+    if galaxy_wait 30; then
         break
     fi
     echo "Galaxy still starting, tailing logs..."
@@ -132,7 +145,7 @@ docker logs httpstest
 sleep 180s && curl -v -k --fail https://127.0.0.1:443/api/version
 echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep localhost
 
-docker stop httpstest && docker rm httpstest
+docker rm -f httpstest || true
 
 # Test FTP Server upload
 date > time.txt
@@ -142,7 +155,9 @@ date > time.txt
 #curl -v --fail ftp://localhost:8021 --user $GALAXY_USER:$GALAXY_USER_PASSWD
 
 # Test SFTP Server
-sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'
+if [[ "$SKIP_SFTP" != "true" ]]; then
+    sshpass -p $GALAXY_USER_PASSWD sftp -v -P 8022 -o User=$GALAXY_USER -o "StrictHostKeyChecking no" localhost <<< $'put time.txt'
+fi
 
 # Test CVMFS
 docker_exec bash -c "service autofs start"
@@ -186,14 +201,18 @@ docker run -d -p 8080:80 \
     quay.io/bgruening/galaxy
 
 echo 'Waiting for Galaxy to come up.'
-galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
+galaxy_wait "$GALAXY_WAIT_TIMEOUT"
 
 # Test if the tool installed previously is available
 curl -v --fail 'http://localhost:8080/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2'
 
 # analyze image using dive tool
-CI=true dive quay.io/bgruening/galaxy
+if [[ "$SKIP_DIVE" == "true" ]]; then
+    echo "Skipping dive image analysis (dive not installed)."
+else
+    CI=true dive quay.io/bgruening/galaxy
+fi
 
 docker stop galaxy
 docker rm -f galaxy
-docker rmi -f $DOCKER_RUN_CONTAINER
+docker rmi -f $DOCKER_RUN_CONTAINER || true

.github/workflows/single_container.yml

@@ -9,6 +9,16 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v6
+    - name: Configure Docker data-root
+      run: |
+        sudo mkdir -p /mnt/docker
+        if [ ! -f /etc/docker/daemon.json ]; then
+          echo '{}' | sudo tee /etc/docker/daemon.json
+        fi
+        sudo jq '."data-root"="/mnt/docker"' /etc/docker/daemon.json > /tmp/docker_daemon.json
+        sudo mv /tmp/docker_daemon.json /etc/docker/daemon.json
+        sudo systemctl daemon-reload
+        sudo systemctl restart docker
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
     - uses: actions/setup-python@v6