Cleaning files with gbrowse-clean and supercronic

compose/gbrowse/README.md

@@ -35,6 +35,7 @@ Then copy all gbrowse2 database data in `/data` directory. Then exit container:
 
 ```
 $ cp -ra /var/lib/gbrowse2/databases/* /data/
+$ chown www-data.www-data /data/
 $ exit
 ```
 
@@ -111,7 +112,7 @@ Then you could copy files like this:
 $ cd /var/lib/gbrowse2/databases
 $ mkdir volvox
 $ cd /var/www/html/gbrowse2/tutorial/
-$ cp data_files/* /var/lib/gbrowse2/databases/volvox/
+$ cp -ra data_files/* /var/lib/gbrowse2/databases/volvox/
 $ cd /var/lib/gbrowse2/databases
 $ chown -R www-data.www-data volvox
 ```

compose/gbrowse/docker-compose.yml

@@ -77,6 +77,30 @@ services:
       - back-tier
 
 
+  supercronic:
+    build: ./gbrowse
+
+    command: ["supercronic", "/etc/cron.d/gbrowse-clean"]
+
+    volumes:
+      - type: volume
+        source: ./gbrowse/conf.d
+        target: /etc/gbrowse2
+
+      - type: bind
+        source: /etc/localtime
+        target: /etc/localtime
+        read_only: true
+
+      - type: volume
+        source: ./gbrowse-data
+        target: /var/lib/gbrowse2/databases
+
+      - type: bind
+        source: gbrowse-cache
+        target: /var/tmp/gbrowse2
+
+
   db:
     # get the latest mysql server
     build: ./db

compose/gbrowse/gbrowse/Dockerfile

@@ -193,5 +193,23 @@ EXPOSE 443
 # add this symlink to work with gbrowse scripts
 RUN ln -s /etc/gbrowse2/ /etc/GBrowse2
 
+# install curl
+RUN apt-get update && apt-get install -y \
+    curl \
+ && rm -rf /var/lib/apt/lists/*
+
+# install supercronic (https://github.com/aptible/supercronic/)
+ENV SUPERCRONIC_URL=https://github.com/aptible/supercronic/releases/download/v0.1.4/supercronic-linux-amd64 \
+    SUPERCRONIC=supercronic-linux-amd64 \
+    SUPERCRONIC_SHA1SUM=3a631023f9f9dd155cfa0d1bb517a063d375055a
+
+RUN curl -fsSLO "$SUPERCRONIC_URL" \
+ && echo "${SUPERCRONIC_SHA1SUM}  ${SUPERCRONIC}" | sha1sum -c - \
+ && chmod +x "$SUPERCRONIC" \
+ && mv "$SUPERCRONIC" "/usr/local/bin/${SUPERCRONIC}" \
+ && ln -s "/usr/local/bin/${SUPERCRONIC}" /usr/local/bin/supercronic
+
+COPY gbrowse-clean /etc/cron.d/gbrowse-clean
+
 # execute apache in foreground
 CMD ["/usr/local/bin/apache2-foreground"]

compose/gbrowse/gbrowse/conf.d/volvox.conf

@@ -18,7 +18,7 @@ examples = ctgA
 initial landmark = ctgA:5000..10000
 
 # Restrict access to registered user
-restrict = require valid-user
+# restrict = require valid-user
 
 ########################
 # Default glyph settings

compose/gbrowse/gbrowse/gbrowse-clean

@@ -0,0 +1,3 @@
+
+# m h  dom mon dow   command
+0 *  *  *  * sudo -u www-data /usr/local/bin/gbrowse_clean.pl