Skip to content

Latest commit

 

History

History
43 lines (29 loc) · 1.63 KB

development.org

File metadata and controls

43 lines (29 loc) · 1.63 KB
Raw

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.