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7 changes: 4 additions & 3 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,10 @@ RUN apk add --update \
heimdal \
&& rm -rf /var/cache/apk/*

#wheel needed by ruamel.yaml for some reason
RUN pip3 install -U wheel setuptools pip
RUN pip3 install cwltool
# wheel needed by ruamel.yaml for some reason
# https://stackoverflow.com/a/75722775
RUN pip3 install --break-system-packages -U wheel setuptools pip
RUN pip3 install --break-system-packages cwltool
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Maybe use pipx instead?

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We can do that too, but then we will have to modify another step above to install it, with sudo apt install pipx I think. Or use another docker multi-stage build image to get python with some virtual env (mamba/pip/etc). Maybe we can create an issue to check which option would work best.

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I think adding pipx to the apt-get install will work easily


RUN cwltool --version

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2 changes: 1 addition & 1 deletion pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<version>1.19.3</version>
<version>1.19.4</version>
<scope>test</scope>
</dependency>
<dependency>
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