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Flow ships with tasks that do not have all of their dependencies included.  On startup Flow will attempt to install the dependencies, but not every system is equipped to install them.

In the case of any difficulties, it is highly recommended to instead use a docker deployment  (cluster installations may require singularity instead, which is somewhat still a work-in-progress)

CNVkit

Requires Python 2.7 or later.

On startup Flow will attempt to install additional python packages using pip.the command pip install --user cnvkit==0.8.5

If pip can not cannot be installed on the target machines then the packages can be downloaded from: 

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On startup Flow will attempt to install additional R packages. 

There are cascading dependencies, but you can view the core libraries in partek_flow/bin/cnvkit-0.8.5/install.R

If these packages can't be built locally, it may be possible for the user to download them from us (see below).

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On startup Flow will attempt to install additional R packages. 

There are cascading dependencies, but you can view the core libraries in partek_flow/bin/deseq_two-3.5/install.R

If these packages can't be built locally, it may be possible for the user to download them from us (see below).

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This is a compiled Perl script (so it has no direct dependency on Perl itself) we have have had one report (istem.fr) of it failing to run. 

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