Mercurial > repos > greg > ideas_genome_tracks
changeset 78:55da56869a0d draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 03 Jan 2018 14:22:09 -0500 |
| parents | 8c4549f123da |
| children | efbc9e58c4eb |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Wed Jan 03 13:59:17 2018 -0500 +++ b/ideas_genome_tracks.R Wed Jan 03 14:22:09 2018 -0500 @@ -26,20 +26,18 @@ args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options -create_primary_html = function(output_trackhub, hub_dir) { - hub_dir_files <- list.files(path=hub_dir); +create_primary_html = function(output_trackhub, tracks_dir, build) { + track_files <- list.files(path=tracks_dir); s <- paste('<html><head></head><body>', sep="\n"); - s <- paste(s, '<h3>Contents of directory ~/myHub', ' required by UCSC TrackHub</h3>\n', sep=""); + s <- paste(s, '<h3>Contents of directory ~/myHub/', build, ' required by UCSC TrackHub</h3>\n', sep=""); s <- paste(s, '<ul>\n', sep="") - for (i in 1:length(hub_dir_files)) { - s <- paste(s, '<li><a href="', 'myHub/', "/", hub_dir_files[i], '">', hub_dir_files[i], '</a></li>\n', sep=""); + for (i in 1:length(track_files)) { + s <- paste(s, '<li><a href="', 'myHub/', build, "/", track_files[i], '">', track_files[i], '</a></li>\n', sep=""); } s <- paste(s, '</ul>\n</body>\n</html>', sep=""); cat(s, file=output_trackhub); } - - create_cells = function(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors) { # Create everything needed, including the bigbed file, # to render the tracks within the UCSC track hub. @@ -219,4 +217,4 @@ write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F); # Create the primary HTML dataset. -create_primary_html(opt$output_trackhub, hub_dir); +create_primary_html(opt$output_trackhub, tracks_dir, opt$build);