| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Changed file permssions to non-executable | Pjotr Prins | |
| 2016-06-18 | Disable setting sys.paths | 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 | |
| 2016-05-17 | Merge branch 'staging' of github.com:genenetwork/genenetwork2 | zsloan | |
| 2016-05-10 | Correlation successfully uses materialized views and parallel processing, ↵ | zsloan | |
| but for some reason is taking an immense amount of time so need to troubleshoot that Changed order of mapping options to display Interval Mapping first Changed some links to no longer open in new tab/window | |||
| 2016-04-20 | A few fixes to get the webserver running again | Pjotr Prins | |
| 2016-04-20 | Parsing the names of the individuals, and coding H as -999 | DannyArends | |
| 2016-04-20 | Adding the geno file parser from Zach | DannyArends | |
| 2016-04-20 | Show error when GENODIR is missing | Pjotr Prins | |
| 2016-04-20 | external program should fail on return value not zero | pjotrp | |
| 2016-04-20 | Minor fixes | pjotrp | |
| 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 | |
| 2016-04-07 | SNP Track option should now work for GN1 mapping figure | zsloan | |
| Fixed typo in show_trait html that caused the p-value slider to not work for correlations | |||
| 2016-04-06 | Permutations (suggestive/significant lines, legend, and histogram) should ↵ | zsloan | |
| now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant | |||
| 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 | |||
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69 | zsloan | |
| Fixes #69 | |||
| 2015-06-29 | Merge pull request #77 from lomereiter/fix_sql | zsloan | |
| SQL security fixes | |||
| 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. | |||
| 2015-06-18 | removed unused function | Artem Tarasov | |
| 2015-06-18 | add missing line to webqtlUtil | Artem Tarasov | |
| 2015-05-12 | Add info to warning | pjotrp | |
| 2015-05-12 | More elaborate handling of finding pylmm | Pjotr Prins | |
| 2015-05-12 | Move path search into tools.py | pjotrp | |
| 2015-05-11 | Moving pylmm out of the tree | pjotrp | |
| 2014-08-12 | Fixed the scrollable data tables for the show trait page | Zachary Sloan | |
| Added the option to display the rqtl results (and soon other mapping results) as either a manhattan plot or "interval map" style curve chart Removed a couple unnecessary javascript imports Changed the function in helper_functions.py that creates the trait and dataset objects, making it to where the trait object also gets qtl info Fixed color by trait after it was broken by the "scatterplot matrix" function | |||
| 2014-07-18 | Added outlier highlighting | Zachary Sloan | |
| Changed order of tabs in statistics panel on trait page Started working on heatmap | |||
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and | Zachary Sloan | |
| adding the correlation matrix page | |||
| 2014-02-27 | Began working on a TraitCollection.py file that will contain both the | Zachary Sloan | |
| object for logged in user collections and collections created by anonymous users. | |||
| 2013-10-17 | Sample objects are now passed to js_data for drawing the correlation | Lei Yan | |
| scatter plot | |||
| 2013-10-11 | Merge /home/sam/gene | Lei Yan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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