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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.
CNVkit
Requires Python 2.7 or later.
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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
Extract this 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)
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On startup Flow will attempt to install additional R packages. If these R packages can not 't be built on the target machine then we can make a set of packages available for download.
Currently, we offer a set of packages compatible with R version 3.4.0: customer.partek.com/R_libs-3.4.0.zip
Extract this file in the home directory. (Make .R a symlink if the home directory doesn't have enough free space)
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 R packages can not 't be built on the target machine then we can make a set of packages available for download.
Currently, we offer a set of packages compatible with R version 3.4.0: customer.partek.com/R_libs-3.4.0.zip
Extract this file in the home directory. (Make .R a symlink if the home directory doesn't have enough free space)
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
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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
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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