For Gemini: Create a master ChromHMM track from the 9 distinct cell types.

make-master-hmm.sh

echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt

# downlaod
for remote in `cat chromhmm-files.txt`
do
	wget $remote
done

# uncompress
for zip in `ls *.gz`
do 
	gunzip -f $zip
done

# bed+ -> ~bedgraph
for bed in `ls *.bed`
do
	cut -f 1-4 $bed > $bed.bedg
done

# union of all intervals across all 9 cell types

bedtools unionbedg -i *.bedg > master.chromhmm.bedg

Remember to tweak the labels for the master bedg. Perhaps some add'l massaging of the values before making it to gemini.

set -ex
cell_types=(Gm12878 H1hesc Hepg2 Hmec Hsmm Huvec K562 Nhek Nhlf)
dir=chromHMM

mkdir -p $dir; cd $dir;

for ct in "${cell_types[@]}"; do
    echo $ct;
    remote=http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmm${ct}HMM.bed.gz
    F=$(basename $remote .gz)
    wget --quiet -O - $remote | zcat - | cut -f 1-4 | perl -pe 's/\d+_(.+)/$1/' > $F
done

bedtools unionbedg -header -names "${cell_types[@]}" -i *.bed > master.chromhmm.bedg