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.

CNVkit

Requires Python 2.7 or later.

On startup Flow will attempt to install additional python packages using pip.

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

customer.partek.com/cnvkit_packages-0.8.5.zip for ubuntu

customer.partek.com/cnvkit_packages-centos7.zip  for centos7

Extract the file in the home directory (Make .local a symlink if the home directory doesn't have enough free space)

Requires R 3.2.3 or later.

On startup Flow will attempt to install additional R packages.  If these packages can't be built locally, it may be possible for the user to download them from us (see below).

DESeq2

Requires R 3.0 or later.

On startup Flow will attempt to install additional R packages.  If these packages can't be built locally, it may be possible for the user to download them from us (see below).

RcppArmadillo may also have dependencies on multi-threading shared objects that may not be on the LD_LIBRARY_PATH

The recommendation is to copy those .so files to a folder and make sure it is available from the LD_LIBRARY_PATH when the server/worker starts.

Additional dynamic libraries (such as libxml2.so) may be missing and we can provide a copy appropriate for the target OS.

Variant Effect Predictor

This is a compiled Perl script, we've have one report (istem.fr) of it failing to run. 

GATK

coming soon

Downloadable R packages

Currently, we offer a set of R packages compatible with some versions of R

• 3.2.3
• 3.4.0
• 3.4.3

Extract this file in the home directory.  (Make .R a symlink if the home directory doesn't have enough free space)

These packages include the dependencies for both CNVkit and DESeq2

see also:  Minimum System Requirements

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