proteowizard/panorama-cruxcometpercolator2limelightxml repository overview

Use cruxCometPercolator2LimelightXML.jar⁠ to convert the results of a Crux Comet + Percolator (https://github.com/crux-toolkit/crux-toolkit⁠) analysis to limelight XML suitable for import into the limelight web application.

The Dockerfile can be used to create a docker image containing:

• cruxCometPercolator2LimelightXML.jar (from https://github.com/yeastrc/limelight-import-crux-comet-percolator/releases⁠)

⁠Usage Examples

⁠Convert Percolator results

docker run -it -v /data/samples/workflows/DDA_CruxCometPercolatorLimelight/testfiles:/data --rm panorama-cruxcometpercolator2limelightxml:latest java -jar /code/cruxCometPercolator2LimelightXML.jar -d /data/crux_output -f /data/Human_PD_ClinVarpep.fasta -o 2020_0212_Loomis_23_DDA_SIM60_515_35.crux.limelight.xml

This assumes that the comet and percolator results are located in the directory /data/samples/workflows/DDA_CruxCometPercolatorLimelight/testfiles/crux_output on your local workstation.

⁠Check the version of cruxCometPercolator2LimelightXML.jar in the docker image

docker run -it --rm panorama-cruxcometpercolator2limelightxml:latest java -jar /code/cruxCometPercolator2LimelightXML.jar --version