| Age | Commit message (Expand) | Author |
|---|
| 2017-08-29 | Mostly changes related to getting gemma working with covariates and BIMBAM fi......Other changes include:
- Fixing links in the network graph
- Changing button colors on show trait page
- Changing color scheme for heatmap
- Making rows highlight in yellow when clicked on
- Some changes to table appearance (like giving gene global search a horizontal scroll)
| zsloan |
| 2017-05-21 | Merge 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 |
| 2017-04-05 | - Temporary traits can be created, viewed, and added to collections...- Correct PCA trait data is created but can't be saved yet
- Added inner margins by increasing xDomain and yDomain of probability plot on trait page
- Increased X/Y-axis label font size
- Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading
- Improved appearance of correlation page table
- Added links to github to index page
- Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those
- Removed "Tissue" from trait page for phenotype traits
| zsloan |
| 2016-10-07 | Saner handling of TMPDIR and TEMPDIR...Throw error when TMPDIRs are not writable
| 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 set......Run with
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
| Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-05-31 | Allow the json dir to be in the old location. | Pjotr Prins |
| 2016-05-26 | Issue with certain samples (like BXD65a, ones were there are multiple for a s......Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments)
Fixed error when searching genotype data sets
| zsloan |
| 2016-05-23 | Reaper mapping results are now correct and account for samples with two names......R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
| zsloan |
| 2016-05-13 | Removing ref. to HTMLPATH | Pjotr Prins |
| 2016-05-13 | WebqtlConfig.py: Constant handling | Pjotr Prins |
| 2016-05-13 | Fix paths for images | Pjotr Prins |
| 2016-04-20 | Add file | Pjotr Prins |
| 2016-02-25 | fixed untracked files | zsloan |
| 2015-12-14 | GN1 mapping full genome figure now correct for pylmm and output to web page | zsloan |
| 2015-12-12 | Changed loop drawing qtl curve to fix some issues; still need to make it draw... | zsloan |
| 2015-07-09 | Mapping methods now check for existing genotype files....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
| zsloan |
| 2015-03-27 | Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ... | zsloan |
| 2015-03-25 | Pair scan image now loads properly | zsloan |
| 2015-03-24 | Change back port location and home directory location; this should be in exte... | zsloan |
| 2015-03-23 | Updates to make GN2 work on my version of penguin (ports, and paths) | DannyArends |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user
password, etc
| Zachary Sloan |
| 2013-07-19 | Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist
| Zachary Sloan |
| 2013-07-18 | Added Amelie's rat data genotypes...Got human mapping mostly working
Fixed dataset dropdown menus
| Zachary Sloan |
| 2013-07-18 | Added to installation notes...Removed webqtlConfigLocal file containing passwords
Updated main page dropdown menus (dataset_menu_structure.json)
| Zachary Sloan |
| 2013-06-13 | Merge /home/sam/gene into flask...Conflicts:
wqflask/wqflask/templates/index_page.html
Merging the code on Sam's branch onto my own
| Zachary Sloan |
| 2013-04-17 | Created file with pickled SNPIterator (from input.py) data...for HLC datasets
Still need to read in file
| Zachary Sloan |
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan |
| 2013-02-07 | Added code to marker_regression.py that creates the numpy arrays to...pass to Nick's code and changed the prep_data.py code to operate on
a list of phenotype values instead of a textfile with the values
delimited
| Zachary Sloan |
| 2013-01-25 | Fixed a few bugs while trying to get the code running on the new server | Zachary Sloan |
| 2012-05-24 | Trying to get stuff working under new structure | Sam Ockman |
