v0.3.1

Author: MattBixley

docker/Dockerfile

@@ -143,14 +143,15 @@ RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11
     rm -rf STAR_2.7.11b*
 
 # Install QualiMap
-RUN wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \
+# RUN wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \
+# the above would not download, so switched to the dropbox link provided by MattB
+RUN wget https://www.dropbox.com/scl/fi/99rhz8q113vwi403bv6ys/qualimap_v2.3.zip \
     unzip qualimap_v2.3.zip && \
     mv qualimap_v2.3 /opt/qualimap && \
     echo '#!/bin/bash\njava -Xms32m -Xmx2g -jar /opt/qualimap/qualimap.jar "$@"' > /usr/local/bin/qualimap && \
     chmod +x /usr/local/bin/qualimap && \
     rm qualimap_v2.3.zip
 
-
 #create a symlink for python as hisat2 hashbangs are set for python and not python3
 RUN ln -s /usr/bin/python3 /usr/bin/python 
 

submit.yml.erb

@@ -13,7 +13,7 @@ script:
   native:
     container:
       name: "rnaseq"
-      image: "ghcr.io/nesi/training-environment-rstudio-rnaseq-app:v0.3.0"
+      image: "ghcr.io/nesi/training-environment-rstudio-rnaseq-app:v0.3.1"
       command: ["/bin/bash","-l","<%= staged_root %>/job_script_content.sh"]
       restart_policy: 'OnFailure'
       env: