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morloc-project / examples

Examples of morloc code and comparisons to other methods
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Dockerfile fails as folder modules is missing #5

Closed stain closed 2 months ago

stain commented 2 months ago

Using docker build workflow-comparisons on Linux Mint 21.3 with podman fails:

WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
--> 48f0d814f00
STEP 7/20: COPY modules /cases-lib
Error: error building at STEP "COPY modules /cases-lib": checking on sources under "/home/stain/dropbox/work/review/peerj/99036-morloc/morloc-project-examples-4b19b6d/workflow-comparisons": copier: stat: "/modules": no such file or directory

It's not clear to me if this refers to ./workflow-comparisons/flu-case-study/modules or another folder as it's a fairly generic folder name.

stain commented 2 months ago

I get same error with make:

(base) stain@xenamint:~/src/examples/workflow-comparisons$ make
docker build -t arendsee/flucase-comparisons .
STEP 1/20: FROM arendsee/morloc:v0.48.0
STEP 2/20: ENV DEBIAN_FRONTEND=noninteractive
--> Using cache f99b09b8ec785e1a7c6b09d4020f07a14241f32f8cc4b7c16823a5149c5c23ac
--> f99b09b8ec7
STEP 3/20: ENV TZ=UTC
--> Using cache 4f06b254525c71073ab47f558f460d4d98d1f84b74118f75ddafde10fd3d150c
--> 4f06b254525
STEP 4/20: RUN    apt-get update     && apt-get install -y libeigen3-dev     && apt-get clean     && python3 -m pip install --upgrade pip setuptools wheel
--> Using cache ccea2b844c15423e17c1b45f6d8d664edddb9875f78e34bf3b91795c8fd390e0
--> ccea2b844c1
STEP 5/20: RUN ln -s /usr/include/eigen3/Eigen /usr/include/Eigen
--> Using cache d3809679532e379ac84f011ba30ca1218af33fc133cdb879957b0e291d7124ca
--> d3809679532
STEP 6/20: RUN pip3 install pybind11 numpy biopython requests rpy2 click
--> Using cache 48f0d814f00aa00410f9c93cc50c6a739f168e7699ee1e1a7fd0f262dbef4e40
--> 48f0d814f00
STEP 7/20: COPY modules /cases-lib
Error: error building at STEP "COPY modules /cases-lib": checking on sources under "/home/stain/src/examples/workflow-comparisons": copier: stat: "/modules": no such file or directory
make: *** [Makefile:5: build] Error 125