galaxy_circos example

test

# enable local perl with perl libraries for circos installed
PATH=/usr/bin:$PATH

python /home/maticzkd/src/galaxy_circos/plot.py \
--output $HOME/test.png \
--circos_path "/home/maticzkd/src/circos-0.67-7/bin/circos -noparanoid" \
--karyotype \
/home/maticzkd/src/circos-0.67-7/data/karyotype/karyotype.drosophila.lowres.dm3.txt \
--cytobands true \
--tracks \
/home/maticzkd/projects/uvCLAP/scratch/150511_circos_plots/data/Gaps_K1_MiSeq/A+B_merged_MLE_wt_junction.nonCanonical_R1+merged_sizes-merged_duplicates-removed_GAPS_ONLY.bedGraph \
/home/maticzkd/projects/uvCLAP/scratch/150511_circos_plots/data/Gaps_K1_MiSeq/A+B_merged_MLE_wt_junction.nonCanonical_R1+merged_sizes-merged_duplicates-removed_GAPS_ONLY.bedGraph \
--types heatmap scatter \
--orientations in in \
--r0 0.9 0.8 \
--r1 0.98 0.88 \
--extend_bins no yes \
--tracks_colors black red \
#--chromosomes dmX

## everything after tracks is required for tracks
## uses absolute paths everywhere
## can use additional parameters to circos in path
## -noparanoid flag is required for plotting the dm3 karyotype from the circos dist