Convert pathways from WikiPathways to CX format and export to NDEx.
Just install Nix. Then when you run
./export.R
the first time, all required dependencies will be installed for
you.
- Clone and enter this repo:
git clone https://github.com/wikipathways/wikipathways2ndex.git
cd wikipathways2ndex
Temporary: until the updated version (>= 3.3.7-7) of the WikiPathways app for Cytoscape is put into production, do this:
bash ./install_dev_wikipathways_app.sh
- Create an account at NDEx if you don't have one. Then set your NDEx username and password (perhaps in
~/.profile
):
export NDEX_USER_UUID="userid-for-your-ndex-account"
export NDEX_USER="username-for-your-ndex-account"
export NDEX_PWD="password-for-your-ndex-account"
If you don't have permissions to edit the NDEx Network Sets specified in wikipathways2ndex.R
,
you'll need to change to one you can edit.
- Execute:
./export.R AnalysisCollection ndex ./output-dir
To see more options, run ./export.R --help
To put job running and detach:
screen -R
./export.R AnalysisCollection ndex ./output-dir
# Ctrl+a
# d
Now you can leave. To check up on the job and then close the screen:
screen -R
# look at what's going on. if the job is complete, you can kill the screen:
# Ctrl+a
# K
Run tests: ./test/test.sh
We used xvfb-run
as a dummy display to enable running Cytoscape in headless mode. Should we use something other than xvfb-run
?
xf86videodummy is maybe supposed to be the replacement for xvfb.
nix-env -iA nixos.xorg.xf86videodummy
It's also possible to use xpra
like xvfb-run
nix-env -iA nixos.xpra
Interesting example of using R or R in X.