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| author | Arun Isaac | 2022-01-03 17:45:14 +0530 |
|---|---|---|
| committer | Arun Isaac | 2022-01-06 10:01:05 +0530 |
| commit | f4e336eb1ea526156e112cff97a3ec8137a2bc90 (patch) | |
| tree | 52f26521904d4c3a158a60f7674a0eb277b09b58 /README.md | |
| parent | 2f0dacc477b2cd239b3da89078476845540de3e7 (diff) | |
| download | genenetwork2-f4e336eb1ea526156e112cff97a3ec8137a2bc90.tar.gz | |
bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.
`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 17 |
1 files changed, 7 insertions, 10 deletions
diff --git a/README.md b/README.md index 972d5c50..d5539a9f 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ genenetwork2 A quick example is ```sh -env GN2_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \ +env SERVER_PORT=5300 \ GENENETWORK_FILES=~/data/gn2_data/ \ GN_PROXY_URL="http://localhost:8080"\ GN3_LOCAL_URL="http://localhost:8081"\ @@ -69,19 +69,16 @@ We are building 'Mechanical Rob' automated testing using Python which can be run with: ```sh -env GN2_PROFILE=~/opt/gn-latest \ - ./bin/genenetwork2 \ +env ./bin/genenetwork2 \ GN_PROXY_URL="http://localhost:8080" \ GN3_LOCAL_URL="http://localhost:8081 "\ ./etc/default_settings.py -c \ ../test/requests/test-website.py -a http://localhost:5003 ``` -The GN2_PROFILE is the Guix profile that contains all -dependencies. The ./bin/genenetwork2 script sets up the environment -and executes test-website.py in a Python interpreter. The -a switch -says to run all tests and the URL points to the running GN2 http -server. +The ./bin/genenetwork2 script sets up the environment and executes +test-website.py in a Python interpreter. The -a switch says to run all +tests and the URL points to the running GN2 http server. #### Unit tests @@ -102,9 +99,9 @@ runcmd coverage html The `runcmd` and `runpython` are shell aliases defined in the following way: ```sh -alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 +alias runpython="env TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 -alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 ./etc/default_settings.py -cli" +alias runcmd="time env TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ GN_PROXY_URL="http://localhost:8080" GN3_LOCAL_URL="http://localhost:8081" ./bin/genenetwork2 ./etc/default_settings.py -cli" ``` Replace some of the env variables as per your use case. |