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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

registry.partek.com/flow_dna

Documentation on installing DECoN is available here:

https://github.com/RahmanTeam/DECoN/blob/master/DECoN-v1.0.2.pdf

DECoN requires R version 3.1.2

It must be installed under /opt/R-3.1.2 or set the DECON_R environment variable to its folder

wget http://cran.wustl.edu/src/base/R-3/R-3.1.2.tar.gz

tar xfz R-3.1.2.tar.gz  

cd R-3.1.2

./configure --with-x=no && make

Download DECoN

https://github.com/RahmanTeam/DECoN/archive/refs/tags/v1.0.2.zip

and install it under /opt/DECoN or set the DECON_PATH environment variable to its folder

You may need to add 

symlink.system.packages: TRUE

to Linux/packrat/packrat.opts

see also:  Minimum System Requirements

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