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* Development
** Using GN2_PROFILE
After cloning the git source tree you can run the contained GN2 using
an existing GN2_PROFILE, i.e., use a profile that was create to run a
binary installation of GN2. This profile may be found by typing
: which genenetwork2
: /home/wrk/opt/gn-latest-guix/bin/genenetwork2
An example of running the development version would be
: env GN2_PROFILE=/home/wrk/opt/gn-latest-guix ./bin/genenetwork2
Profiles are stored in /gnu/store, so you may pick one up there
: readlink -f $(dirname $(dirname `which genenetwork2`))
: /gnu/store/dvckpaw770b00l6rv4ijql8wrk11iypv-profile
and use that instead.
Note that the genenetwork2 script sets up the environment for running
the webserver. This includes path to R modules and python modules. These
are output on startup. To make sure there is no environment pollution you can
** Javascript modules
As of release 2.10-pre4 we Javascript modules are installed in three places:
1. JS_GUIX_PATH: the Guix store - these are Guix pre-packaged modules
2. The git source tree (./wqflask/wqflask/static/packages/)
3. JS_GN_PATH: a local directory containing (temporary) development modules
Packages currently in git (2) will move to JS_GUIX_PATH (1) over
time. This is to keep better track of origin updates. Putting packages
in git (2) is actively discouraged(!), unless there are GN2 specific
adaptations to the original Javascript modules.
JS_GN_PATH (3) is for development purposes. By default is is set to
$HOME/genenetwork/javascript. Say you are working on an updated
version of a JS module not yet in (1) you can simply check out that
module in that path and it should show up.
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