morinlab / galaxy_tools Goto Github PK

Update Galaxy tool to contain the new multiplot colour scheme for variant classes

Despite creating Anaconda 3 packages in #18, I'm creating separate conda installations using Miniconda 3 for morinkit. This is based on the recommendation in the readme for the iuc anaconda package.

Care should be taken in using the Anaconda Python environment that is installed by this recipe. Other recipes should not be used to install additional Python packages into this environment as doing so will adversely impact reproducibility for tools that depend on this package. Installation recipes that take advantage of the Anaconda Python environment (but that need additional packages) should be written as separate, self-contained recipes.

Use Strelka and Titan Results

use the Manta SV data

Working off of https://testtoolshed.g2.bx.psu.edu/view/iuc/package_anaconda_2_3_0/d3f29b11da06

Apply Expands to exomes with known subclonal structure and assess how well this is resolved and how well individual mutations get assigned to their correct cluster (if we can access this info?)

Required Steps

• Create minimum working protoypes of ensemble_caller (see BrunoGrandePhD/ensemble_caller#2).
• Upload ensemble_caller to PyPI (see BrunoGrandePhD/ensemble_caller#3).
• Create Galaxy wrapper/tool.

Functions:

• plotmafSummary
• oncoplot
• plotTiTv
• lollipopPlot
• rainfallPlot
• geneCloud
• gisticPlot
• plotGisticResults

The following table lists the tools we need to push to the Test Toolshed. Update the assignee and status accordingly.

Obtain or create a MAF file that can be used to run Comet on the command line. Use the resulting output for testing the comet wrapper on galaxy.

so that PyClone, GISTIC, EXPANDS, etc can use scripts in that repo