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2016-04-20Adding initial file to perform CTL analysisDannyArends
2016-04-20[PATCH 078/100] Adding empty templates for CTL in GN2DannyArends
2016-04-20Cleaning up the WGCNA parameter input templateDannyArends
2016-04-20[PATCH 061/100] Put R/qtl .cross file in TMPDIRPjotr Prins
2016-04-20Show error when GENODIR is missingPjotr Prins
2016-04-20Remove dbdocpjotrp
2016-04-20Removed symlinkspjotrp
2016-04-20r-wgcna: Fix pathspjotrp
2016-04-20More hard-codedpjotrp
2016-04-20[PATCH 050/100] Using out-of-tree storage. Added comments for plink,Pjotr Prins
gemma.
2016-04-20[PATCH 049/100] SNP_PATH: removalPjotr Prins
2016-04-20[PATCH 047/100] This commit moves the image generation dir *outside* the git ↵Pjotr Prins
repository.
2016-04-20external program should fail on return value not zeropjotrp
2016-04-20[PATCH 045/100] Reverted on previous changes. With a correctedPjotr Prins
python2-piddle module the thing works. Turns out that the version we are using is not the same as the public one. Despite the same version number.
2016-04-20Minor fixespjotrp
2016-04-20[PATCH 042/100] Sanitizing locationsPjotr Prins
2016-04-20[PATCH 041/100] Fixes for running toolsPjotr Prins
2016-04-20When a sample does not exist we should not set sample_data to None. Better ↵pjotrp
to leave it out so it never gets processed again.
2016-04-20-aPjotr Prins
[PATCH 039/100] Removing commented code
2016-04-20-aPjotr Prins
[PATCH 038/100] Fix compile errors
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-04-20Settled on the _COMMAND syntax over _RUNpjotrp
2016-04-20With missing samples to not add them to the result setpjotrp
2016-04-20This threw an error when sample is missing in the DB.pjotrp
Let sample pass without data if the sample/genotype does not exist in the database.
2016-04-20[PATCH 033/100] Refactored file searchingPjotr Prins
2016-04-20[PATCH 032/100] file locating: error checking is built-inPjotr Prins
2016-04-20Fine tuning file locatingpjotrp
2016-04-20tools.py: add function locate_without_errorpjotrp
2016-04-20[PATCH 027/100] Introduce tools.locatePjotr Prins
2016-04-20[PATCH 026/100] Introducing cached values PYLMM_COMMAND,Pjotr Prins
GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
2016-04-20Introducing TEMPDIRpjotrp
2016-04-20[PATCH 024/100] Sanitizing file handlingPjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
2016-04-20Remover dependency to logger_tree (may reintroduce later)pjotrp
2016-04-20[PATCH 018/100] Find external tools: refactored code to work with GNU GuixPjotr Prins
2016-04-20Removed import htmlgen as is not used (apparently)pjotrp
2016-04-18Additive effect lines are now separated by chromosome (like the qtl line in ↵zsloan
the last commit) Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later
2016-04-14Fixed issue where qtl lines in interval mapping wouldn't connect between ↵zsloan
chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits
2016-04-13Moved the code getting the description/location because it was throwing an ↵zsloan
error for phenotype traits
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Changed the way trait data is retrieved for the global search page (it now ↵zsloan
gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-04-07Added option to change the maximum y-axis value for GN1 mapping figurezsloan
2016-04-07Permutation figure and x-axis label should change to correctly reflect the ↵zsloan
mapping scale (lrs or lod) Fixed bug where broken image link would appear if you ran R/qtl with no permutations
2016-04-07SNP Track option should now work for GN1 mapping figurezsloan
Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06The option to switch between LRS and LOD for the GN1 mapping figure should ↵zsloan
now work correctly. The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
2016-04-06Setting lodm to always be 1.0 fixes the issue where it would incorrectly ↵zsloan
display LOD scores for the Y-Axis instead of LRS values
2016-04-06Permutations (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
2016-04-05Bootstrap test should now work correctly for qtl reaper mapping method on ↵zsloan
full genome view There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
2016-04-05Fixed issue where haplotype analyst option would appear when using ↵zsloan
genetic(centimorgan) mapping
2016-03-30Disabled Haplotype Analyst option if mapping scale is centimorgan/geneticzsloan
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