| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2016-10-12 | JS: check for file explicitely | Pjotr Prins | |
| 2016-10-12 | JS: check for file explicitely | Pjotr Prins | |
| 2016-10-12 | JS: check for file explicitely | Pjotr Prins | |
| 2016-10-11 | Modified JS paths | Pjotr Prins | |
| Merge branch 'testing' into chfi | |||
| 2016-10-11 | Merge branch 'pjotr-gn2' into testing | Pjotr Prins | |
| 2016-10-09 | Add version information | Pjotr Prins | |
| 2016-10-07 | Make sure JS path exists | Pjotr Prins | |
| 2016-10-07 | Changed error output | Pjotr Prins | |
| 2016-10-07 | Saner handling of TMPDIR and TEMPDIR | Pjotr Prins | |
| Throw error when TMPDIRs are not writable | |||
| 2016-10-03 | Config: supporting JSON OVERRIDES | Pjotr Prins | |
| 2016-10-03 | Debug: sanitize some output | Pjotr Prins | |
| 2016-09-25 | Make sure MAPPING_PATH exists | Pjotr Prins | |
| 2016-09-25 | tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2 | Pjotr Prins | |
| 2016-09-10 | Support for running maintenance scripts so they can pick up all webserver ↵ | Pjotr Prins | |
| settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py | |||
| 2016-06-24 | Log: and document SQL calls | Pjotr Prins | |
| 2016-06-23 | Logger: improved logging | Pjotr Prins | |
| 2016-06-23 | Settings: add GN_SERVER_URL | Pjotr Prins | |
| 2016-06-21 | logger: add format field (reserve) | Pjotr Prins | |
| 2016-06-21 | Logger: switch for logging SQLALCHEMY | Pjotr Prins | |
| 2016-06-21 | Benchmarking: allow output select with LOG_BENCH | Pjotr Prins | |
| 2016-06-19 | gn_server: SQL handling | Pjotr Prins | |
| 2016-06-19 | Renamed settings so they are grouped together | Pjotr Prins | |
| 2016-06-18 | Logging settings | Pjotr Prins | |
| 2016-06-18 | Logger: more info | Pjotr Prins | |
| 2016-06-18 | Logger: introducing logging | Pjotr Prins | |
| 2016-06-18 | Logging: behaviours | Pjotr Prins | |
| 2016-06-18 | Logger: improving output | Pjotr Prins | |
| 2016-06-18 | Logger: introducing logging | Pjotr Prins | |
| 2016-06-17 | Conflict | Pjotr Prins | |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins | |
| 2016-06-16 | Introduce behaviour parameters to facilitate development | Pjotr Prins | |
| 2016-04-20 | A few fixes to get the webserver running again | Pjotr Prins | |
| 2016-04-20 | Show error when GENODIR is missing | Pjotr Prins | |
| 2016-04-20 | [PATCH 042/100] Sanitizing locations | Pjotr Prins | |
| 2016-04-20 | [PATCH 041/100] Fixes for running tools | Pjotr Prins | |
| 2016-04-20 | -a | Pjotr Prins | |
| [PATCH 038/100] Fix compile errors | |||
| 2016-04-20 | [PATCH 037/100] WebQtlConfig: sanitizing naming and used vars | Pjotr Prins | |
| 2016-04-20 | Settled on the _COMMAND syntax over _RUN | pjotrp | |
| 2016-04-20 | [PATCH 033/100] Refactored file searching | Pjotr Prins | |
| 2016-04-20 | Fine tuning file locating | pjotrp | |
| 2016-04-20 | tools.py: add function locate_without_error | pjotrp | |
| 2016-04-20 | [PATCH 027/100] Introduce tools.locate | Pjotr Prins | |
| 2016-04-20 | [PATCH 026/100] Introducing cached values PYLMM_COMMAND, | Pjotr Prins | |
| GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR | |||
| 2016-04-20 | Introducing TEMPDIR | pjotrp | |
| 2016-04-20 | [PATCH 024/100] Sanitizing file handling | Pjotr Prins | |
| 2016-04-20 | [PATCH 023/100] WIP fixing all paths | Pjotr Prins | |
| 2016-04-20 | [PATCH 018/100] Find external tools: refactored code to work with GNU Guix | Pjotr Prins | |
| 2015-11-09 | Fixed issue that caused mapping to not work; for some reason the path to ↵ | zsloan | |
| pylmm was wrong | |||
| 2015-07-09 | Mapping methods now check for existing genotype files. | zsloan | |
| Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory | |||
| 2015-06-26 | Fixed bug where mapping results sometimes wouldn't display. This would occur | zsloan | |
| due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is. | |||
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