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On startup Flow attempts to install using pip
MACS3
Requires python 3.0 or above
pip install --user numpy==1.19.5 Cython==0.29.30 cykhash==2.0.0 macs3==3.0.0a7
Python
If there are any conflicts with preinstalled python packages, Flow should be configured to run with its own virtual environment:
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unizp -d ~/.partekflow/ python-dependencies.zip
Variant Effect Predictor
This is a compiled Perl script (so it has no direct dependency on Perl itself) we have had one report (istem.fr) of it failing to run.
R
R can usually be installed from the package manager. If the user installs Flow via apt or yum it should already be installed.
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packageVersion("packageName")
R_HOME=/path/to/R
Variant Effect Predictor
This is a compiled Perl script (so it has no direct dependency on Perl itself) we have had one report (istem.fr) of it failing to run.
DECoN
DECoN comes pre-installed in the flow_dna container
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