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| author | Arun Isaac | 2023-12-30 09:27:49 +0000 |
|---|---|---|
| committer | Arun Isaac | 2024-01-02 13:40:56 +0000 |
| commit | ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3 (patch) | |
| tree | ba7d697312dea528847f04f1066e173dae905912 /doc | |
| parent | 26f17e7fff8d78ebb10528456fdbb9dee67c24d1 (diff) | |
| download | genenetwork2-ff679636d3ee9ae2388fab3fe5d091ef2f00a8e3.tar.gz | |
Move default settings into gn2 module.
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/GUIX-Reproducible-from-source.org | 4 | ||||
| -rw-r--r-- | doc/development.org | 2 | ||||
| -rw-r--r-- | doc/testing.org | 4 |
3 files changed, 5 insertions, 5 deletions
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index fffa9571..50abec3a 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -252,7 +252,7 @@ Inside the repository: : ./bin/genenetwork2 Will fire up your local repo http://localhost:5003/ using the -settings in ./etc/default_settings.py. These settings may +settings in ./gn2/default_settings.py. These settings may not reflect your system. To override settings create your own from a copy of default_settings.py and pass it into GN2 with @@ -265,7 +265,7 @@ software. If something is not working, take a hint from the settings file that comes in the Guix installation. It sits in something like -: cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py +: cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/gn2/default_settings.py ** Set up nginx port forwarding diff --git a/doc/development.org b/doc/development.org index cd3beea3..4f3693ee 100644 --- a/doc/development.org +++ b/doc/development.org @@ -86,7 +86,7 @@ In fact you can kick off a Python shell with something like env SERVER_PORT=5013 WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ SQL_URI=mysql://gn2:webqtl@localhost/db_webqtl_s \ GN2_PROFILE=~/opt/genenetwork2 \ - ./bin/genenetwork2 ./etc/default_settings.py -c + ./bin/genenetwork2 ./gn2/default_settings.py -c Python 2.7.17 (default, Jan 1 1970, 00:00:01) [GCC 7.5.0] on linux2 Type "help", "copyright", "credits" or "license" for more information. diff --git a/doc/testing.org b/doc/testing.org index d5ab117d..5c1e954e 100644 --- a/doc/testing.org +++ b/doc/testing.org @@ -35,14 +35,14 @@ Run the tests from the root of the genenetwork2 source tree as. Ensure that Redis and Mariadb are running. To run Mechanical Rob: -: time env GN2_PROFILE=~/opt/genenetwork2 TMPDIR=~/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -c ~/projects/genenetwork2/test/requests/test-website.py -a http://localhost:5004 +: time env GN2_PROFILE=~/opt/genenetwork2 TMPDIR=~/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./gn2/default_settings.py -c ~/projects/genenetwork2/test/requests/test-website.py -a http://localhost:5004 Use these aliases for the following examples. #+begin_src sh alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 -alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli" +alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./gn2/default_settings.py -cli" #+end_src You could use them in your =.bashrc= or =.zshrc= file. |