java update

kubernetes/Dockerfile

@@ -41,9 +41,9 @@ RUN curl -s https://get.sdkman.io | bash
 RUN chmod a+x "$HOME/.sdkman/bin/sdkman-init.sh"
 RUN echo "sdkman_auto_complete=false" >> "$HOME/.sdkman/etc/config"
 RUN source "$HOME/.sdkman/bin/sdkman-init.sh" &&\
-	sdk install java 11.0.11.hs-adpt &&\
- 	sdk install gradle 7.1 && \
- 	sdk install maven 3.6.3 && \
+	sdk install java 17.0.1-tem &&\
+ 	sdk install gradle 7.3.1 && \
+ 	sdk install maven 3.8.4 && \
 	rm  -r /root/.sdkman/archives
 
 # R
@@ -88,7 +88,7 @@ RUN source /root/miniconda/bin/activate && \
 	rm /picrust2_env.yml /v2.4.1.tar.gz
 
 ## eggmapper
-RUN pip install eggnog-mapper
+# RUN pip install eggnog-mapper
 
 ## HUMAnN meta-omics
 RUN	python3 -m pip install humann --no-binary :all: && \ 

kubernetes/run.sh

@@ -41,10 +41,11 @@ yaml_file_name="$(basename "$yaml")"
 # Download the yaml file $1=yaml full path
 mkdir -p $yaml_dir
 # Delete yaml file if already exists
-rm $yaml
+rm -f $yaml
 
 # Updating metadata by removing all cwl and cwl path status
 python3 /scripts/metadata.py -key cwl -value $cwl -remove -file $yaml
+
 # Adding the running status
 python3 /scripts/metadata.py -key cwl -value $cwl -unit running -add -file $yaml
 

kubernetes/scripts/metadata.py

@@ -46,6 +46,8 @@ with iRODSSession(
     zone = zone,
     **ssl_settings) as session:
 
+    print("Connected to iRODS ", session.server_version)
+
     obj = session.data_objects.get(args.file)
     # Adding requires full triple
     if args.add: