| Age | Commit message (Collapse) | Author |
|---|
|
in http://files.genenetwork.org/data_files/ and can be used when
unpacked in GENENETWORK_FILES (see ./etc/default_settings.py)
|
|
seems to be related to some strains being renamed in the genofiles
Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days
Updated genofiles
|
|
|
|
|
|
single BXD or whatever) should be fixed for different mapping methods and data set types
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
|
|
reason
|
|
Conflicts:
.gitignore
|
|
|
|
not work because of the new dataset_menu_structure.json file
An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
|
|
pylmm was wrong
|
|
incorrectly converted to json
Fixed GO search to work with combined searches
|
|
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
|
|
Added GEMMA and necessary plink-format genotype files in gemma directory
Added the GEMMA genotype files to git LFS
Removed some unnecessary/duplicated code from interval_mapping.py
Separated GEMMA mapping code into its own file (will also do this for other methods) and fixed
and issue that caused it to not run
Added the table to the pair scan results page and wrote some code adding its attributes
to each marker object, but it still isn't working yet
|
|
where rat trait pages wouldn't work
|
|
directory to 'genotype_files'
|
