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2022-01-28Update PYTHONPATH...The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).zsloan
2022-01-28Revert 'bin: Set shebang to sh instead of bash'...It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash): ./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpectedzsloan
2022-01-28Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."...This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90. Arun Isaac
2022-01-28Revert "bin: Do not set environment variables set by guix shell."...This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8. Arun Isaac
2022-01-27Fix 'Bad substitution' issue...In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation. Frederick Muriuki Muriithi
2022-01-06bin: Stop execution on error....* bin/genenetwork2: Pass -e flag to sh. Arun Isaac
2022-01-06bin: Set shebang to sh instead of bash..../bin/sh is present on Guix System and other distros while /bin/bash is present only on other distros. * bin/genenetwork2: Set shebang to sh instead of bash. Arun Isaac
2022-01-06bin: Do not set environment variables set by guix shell....The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally. Arun Isaac
2022-01-06bin: 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. Arun Isaac
2021-12-01Introduce GN3_PYTHONPATH environment variablePjotr Prins
2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-08-06gunicorn production settings: increase process refresh rate to clean up RAM. ......the jitter switch. Pjotr Prins
2020-08-20Replace all references to python2.7 with python3.8...Run: ``` find . -type f -print0 | xargs -0 sed -i \ "s|lib/python2.7/site-packages|lib/python3.8/site-packages|g" ``` BonfaceKilz
2020-07-25Updating docs and show how to include a local Python modulePjotr Prins
2020-05-12Remove eventletepysodePjotr Prins
2020-04-26Merge master and testingmasterPjotr Prins
2019-09-24Fixed issue that caused logging in to stop working with new GUIX build...Removed some unused JS libraries zsloan
2019-02-13Removed pylmm references and related functionsPjotr Prins
2018-11-20Added option to select chromosome from trait page when mapping...Put transform/blocking tools into their own tab (still need to change formatting of tab's contents) Improved appearance of search result page table (still need to change a few other tables) Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool Basic Stats figures now load when the user clicks the tab, to improve initial page load time zsloan
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ju......- Cofactor color picker now works in Safari/Macs - Displays N for relevant samples in trait page sample table - Don't show bar chart when N>256 - Mapping loading page contents better centered - Anonymous collections timeout correctly listed as 30 days now - Minor allele frequency can actually be changed for GEMMA now (previously didn't work) - Fixed transcript position marker location for mapping results - Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password - Users can now map with submitted traits - Histogram width changes depending upon number of bins (need to improve this still) - Improved Q-q plot (previously called "probability plot") zsloan
2018-09-05Production updatesGN2
2018-04-16Docs on elasticsearch usePjotr Prins
2018-04-12README and docsPjotr Prins
2018-04-04ES: docPjotr Prins
2018-04-02Testing moved to PythonPjotr Prins
2018-03-26- Disabled PYTHONPATH injection - fix Guix instead, see https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS Pjotr Prins
2018-03-26Requests addedPjotr Prins
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no PYTHONPAT......it is now in the Guix build. Pjotr Prins
2018-03-26Fix conflictPjotr Prins
2018-03-26Add elasticsearch module to the path...* Add some code to set up the path for the python-elasticsearch module. Muriithi Frederick Muriuki
2018-02-11Added gunicorn pid so we can not run twicePjotr Prins
2018-02-11Using eventlet workerszsloan
2018-02-10Fix env variable $GEMMA_WRAPPER_COMMANDPjotr Prins
2018-02-10Fixing GEMMA LOCOPjotr Prins
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
2018-01-31Startup: longer timeout for gunicorn-dev modePjotr Prins
2018-01-31Startup: added -cli optionPjotr Prins
2018-01-30gunicorn dev and prod modes addedPjotr Prins
2018-01-29Fixed gunicorn examplePjotr Prins
2018-01-29Gunicorn worksPjotr Prins
2018-01-29startup script: adapting for gunicornPjotr Prins
2018-01-29Added checks in startup script, removed r-auwerx pathPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-09-14./bin/genenetwork2: add GEM_PATH for gemma-wrapperPjotr Prins
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
2017-06-02settings: GENENETWORK_FILESPjotr Prins
2017-05-31JS module handlingPjotr Prins
2017-05-21Merge from the diet branch.... * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile Pjotr Prins
2016-10-09Tests: change optionsPjotr Prins
2016-10-09Add version informationPjotr Prins
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