Mercurial > repos > greg > ideas_genome_tracks
changeset 68:06401685fb92 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 20 Dec 2017 13:00:19 -0500 |
| parents | 1a39146a0cea |
| children | f520807e9cfe |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Wed Dec 20 13:00:07 2017 -0500 +++ b/ideas_genome_tracks.R Wed Dec 20 13:00:19 2017 -0500 @@ -15,6 +15,7 @@ make_option(c("--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"), make_option(c("--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path"), make_option(c("--output_trackhub_id"), action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"), + make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"), make_option(c("--short_label"), action="store", dest="short_label", help="Hub short label"), make_option(c("--state_colors"), action="store", dest="state_colors", default=NULL, help="List of state_colors"), make_option(c("--state_indexes"), action="store", dest="state_indexes", default=NULL, help="List of state_indexes") @@ -178,7 +179,8 @@ write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F); # Create the tracks. -source("create_heatmap.R"); +heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/"); +source(heatmap_path); tracks_dir <- paste(hub_dir, opt$build, "/", sep=""); dir.create(tracks_dir, showWarnings=FALSE); track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_state, opt$input_dir_state, opt$build,