-
Notifications
You must be signed in to change notification settings - Fork 2
Controlled Instance
This document describes the installation of the routine PGx analysis pipeline (gtx R package) in GSK’s Global Data Center (GDC). It includes details on how the installation is configured and is intended primarily for administrators but may also be a useful reference for users.
The pipeline is implemented as an R package with source code maintained on GitHub: https://github.com/tobyjohnson/gtx (may be moved in future from Toby’s account to StatGenPRD – check there if this link is dead). Use of GitHub is well documented on the site and GSK's installation of git is well documented on the internal wikis.
Access to the GDC Linux environment is primarily through us1us0168.corpnet2.com. A controlled instance of the package is installed at
GDC: /GWD/appbase/projects/statgen/GXapp/G-P_assoc_pipeline/R-packages/x86_64-unknown-linux-gnu-library/3.0/gtx
By controlled instance, we mean edit access is restricted to the gxappdev group. Anyone attempting to change this instance should be fully aware of the potential downstream consequences (e.g. an upgrade of the package may require re-validation). Additionally, any changes should be followed by a confirmation / resetting of the permissions such that only the gxappdev group has edit access. Changes should never happen while a user is running an analysis. Assuming all users are following the instructions on running, they should be using SGE and you can check if any jobs are in progres by running
qstat –u "*"
When an administrator does wish to update the controlled instance, this script can be used to build and install from GitHub and reset the permissions
/GWD/appbase/projects/statgen/GXapp/G-P_assoc_pipeline/GDCgtx/package_update/build_install.sh >/GWD/appbase/projects/statgen/GXapp/G-P_assoc_pipeline/GDCgtx/package_update/build_install.out 2>/GWD/appbase/projects/statgen/GXapp/G-P_assoc_pipeline/GDCgtx/package_update/build_install.err
We have opted to use the "local" R3 instance at
GDC: /GWD/appbase/projects/statgen/R3.0.0/R-3.0.0
because it was compiled with cairo graphics enabled which makes generation of high density plots (e.g. QQ and Manhattan) relatively fast. In order to use the "central" R2.14 instance (/GWD/bioinfo/tools/bin/R64-2.14.0) which was not compiled with cairo graphics enabled, a local install of the Cairo package would need to be referenced or else the gtx pipeline will default to PDF for plotting which will be very slow for high density plots and create very large files that are difficult to open.
The gtx pipeline requires several R packages and will optionally use others as available (e.g. Cairo, knitr). These are currently not controlled but instead installed in the "local" R3 instance. In lieu of controlling these, we will report the versions used in the log of each run. Note, currently these are not logged - proposed change here.