Dockerfile to create a streamlit server with OpenMS+pyOpenMS (batteries included)

[timosachsenberg]

The container created by the Dockerfile provides:

• OpenMS library + TOPP tools
• pyOpenMS
• Thirdparty tools
• a streamlit server
• example streamlit pyOpenMS app

User can configure arguments: repository, branch and exposed port.
Note: for releases the docker file could be shorter and just install e.g. the official conda packages etc. but I think this is the most generic approach

[timosachsenberg]

BTW. Instead of creating it on a local computer one can also use gitpod to create the docker files

and preview the app from gitpod by clicking on the link in the gitpod port view:

[jpfeuffer]

As discussed the note about nightly Openms is not optimal.
Either change or remove

[timosachsenberg]

@jpfeuffer what should be pinned here?
I guess the OpenMS and pyOpenMS versions?
streamlit version probably as well
what about the others?

It currently installs:

• pyopenms=2.8.0
• openms=2.8.0 # openms executables
• openms-thirdparty=2.8.0 # e.g. third-party tools, search engines, percolator, ...
• streamlit=1.23.1
• streamlit_plotly_events=0.0.6
• streamlit_aggrid=0.3.4

[jpfeuffer]

Interesting. Shouldn't 2.9.1 be the latest bioconda?

[timosachsenberg]

https://pastebin.com/FieEN8gA

[timosachsenberg]

maybe need a conda --update all

[jpfeuffer]

Sounds unusual for a fresh install of mambaforge

[jpfeuffer]

Why python 3.10 suddenly? In your dockerfile you specify 3.9.

[timosachsenberg]

was just checking something...
as you pointed out the R-base depndency in openms-thirdparty has conflicting dependencies

[timosachsenberg]

@enetz or @jpfeuffer do you know how to fix this step. I guess it picks up the wrong cython or doesn't find it....

 > [35/45] RUN /bin/bash -c "cmake -DCMAKE_PREFIX_PATH='/contrib-build/;/usr/;/usr/local' -DOPENMS_CONTRIB_LIBS='/contrib-build/' -DHAS_XSERVER=Off -DBOOST_USE_STATIC=OFF -DPYOPENMS=On ../OpenMS -DPY_MEMLEAK_DISABLE=On":

#39 1.442 CMake Error at src/pyOpenMS/CMakeLists.txt:131 (message):
#39 1.442   Cython import failed for the given Python executable.
#39 1.442 
#39 1.442 
#39 1.443 -- Configuring incomplete, errors occurred!

[timosachsenberg]

cmake -DCMAKE_PREFIX_PATH='/contrib-build/;/usr/;/usr/local' -DOPENMS_CONTRIB_LIBS='/contrib-build/' -DHAS_XSERVER=Off -DBOOST_USE_STATIC=OFF -DPYOPENMS=On ../OpenMS -DPY_MEMLEAK_DISABLE=On
-- Configuring incomplete, errors occurred!
root@b279fe3be89a:/openms-build# grep py CMakeCache.txt 
CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy
//Do not bundle dependencies into pyOpenMS build folder and wheel
//Do not bundle share into pyOpenMS build folder and wheel
//setup build system for pyOpenMS
pyOpenMS_BINARY_DIR:STATIC=/openms-build/src/pyOpenMS
pyOpenMS_IS_TOP_LEVEL:STATIC=OFF
pyOpenMS_SOURCE_DIR:STATIC=/OpenMS/src/pyOpenMS
//OpenMS Git branch for pyopenms setup.py
FIND_PACKAGE_MESSAGE_DETAILS_Python:INTERNAL=[/usr/bin/python3.10][/usr/include/python3.10][cfound components: Interpreter Development.Module ][v3.10.6()]
_Python_EXECUTABLE:INTERNAL=/usr/bin/python3.10
_Python_INCLUDE_DIR:INTERNAL=/usr/include/python3.10
_Python_INTERPRETER_PROPERTIES:INTERNAL=Python;3;10;6;64;;cpython-310-x86_64-linux-gnu;abi3;/usr/lib/python3.10;/usr/lib/python3.10;/usr/lib/python3/dist-packages;/usr/lib/python3/dist-packages

[timosachsenberg]

root@b279fe3be89a:/usr/bin# pip install Cython
Requirement already satisfied: Cython in /root/mambaforge/lib/python3.10/site-packages (0.29.35)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
root@b279fe3be89a:/usr/bin# which python
/root/mambaforge/bin/python
root@b279fe3be89a:/usr/bin# which python3.10
/root/mambaforge/bin/python3.10

[timosachsenberg]

seems I got it working by only using python etc. from conda

[timosachsenberg]

Template is complete and streamlit server works.

[timosachsenberg]

Done after merge:

• update submodule in streamlit-deployment repo
• provide repo, branch and port arguments in docker compose file in streamlit-deployment repo
  e.g.

    environment:
      - PORT=8501

[enetz]

Other than those two minor comments, this looks good

[timosachsenberg]

we could also think about having mono and ThermoRawFileParser installed on the simple Dockerfile.
Would make it much more convenient for raw file reading/conversion to mzML in the simple case...

[timosachsenberg]

updated streamlit-deployment repo and added two container to compose file

[jpfeuffer]

You could have specified -DPython_EXECUTABLE specifically but I'm glad it's working.