Commit ef00a80a authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

version bump and run cwltool update

parent 41c8de6a
......@@ -33,19 +33,14 @@ RUN pip install python-irodsclient --upgrade && \
echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" | tee -a /etc/apt/sources.list.d/renci-irods.list && \
apt-get update && apt-get install -y irods-icommands
# Install Java via sdkman
# RUN apt-get update
# RUN apt-get -qq -y install \
# curl \
# unzip \
# zip
RUN rm /bin/sh && ln -s /bin/bash /bin/sh
#RUN apt-get -qq -y install curl
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 11.0.9.hs-adpt &&\
sdk install gradle 6.7 &&\
sdk install java 11.0.11.hs-adpt &&\
sdk install gradle 7.1 &&\
sdk install maven 3.6.3
# Other packages
......
......@@ -61,14 +61,11 @@ grep "[0-9]\+_irods:" $yaml | awk '{print $2}' | sort | uniq | awk '{print "java
# Run workflow with or without provenance
if $prov; then
cwltool --basedir /unlock/rancher --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path --provenance $destination_path/PROVENANCE $cwl $yaml
cwltool --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path --provenance $destination_path/PROVENANCE $cwl $yaml
else
cwltool --basedir /unlock/rancher --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path $cwl $yaml
cwltool --tmpdir-prefix /unlock/rancher/unlockcwl --no-container --preserve-entire-environment --outdir $destination_path $cwl $yaml
fi
# Temporary disabled
# --debug --cachedir $destination_path/CACHE_$yaml_file_name/
# Check exit status of cwl
exit_status=$?
......@@ -104,4 +101,4 @@ fi
echo "Removing irods files"
grep "[0-9]\+_irods:" $yaml | awk '{print "rm -f "$2}' | sh
exit 0
\ No newline at end of file
exit 0
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