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author | Lei Yan | 2017-06-26 19:40:09 +0000 |
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committer | Lei Yan | 2017-06-26 19:40:09 +0000 |
commit | 10e3996ad0f1da29dd6f27ec3c10aa6d8660ed03 (patch) | |
tree | 59eba8bb4f99087854d6004648023b05e0a69b38 /doc/development.org | |
parent | afd2028e0ddab64e433eceb19e8cbd8d7149e080 (diff) | |
parent | e467c3f19824415d9e9a3fdd4073d44439c83cbf (diff) | |
download | genenetwork2-10e3996ad0f1da29dd6f27ec3c10aa6d8660ed03.tar.gz |
Merge branch 'master' of github.com:genenetwork/genenetwork2
Diffstat (limited to 'doc/development.org')
-rw-r--r-- | doc/development.org | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/doc/development.org b/doc/development.org new file mode 100644 index 00000000..5e6e318b --- /dev/null +++ b/doc/development.org @@ -0,0 +1,43 @@ +* 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. |