git clone https://github.com/samtools/htslib.git
cd htslib
make
cd .. 
git clone https://github.com/ryanlayer/giggle.git
cd giggle
make

wget http://ftpmirror.gnu.org/libmicrohttpd/libmicrohttpd-0.9.46.tar.gz
tar zxvf libmicrohttpd-0.9.46.tar.gz
cd libmicrohttpd-0.9.46
./configure --prefix=$HOME/usr/local/
make
make install

git clone https://github.com/json-c/json-c.git
cd json-c
sh autogen.sh
./configure --prefix=$HOME/usr/local/
make
make install

cd giggle
make
make server

mkdir data
cd data

wget http://www.gtexportal.org/static/datasets/gtex_analysis_v6/annotations/GTEx_Data_V6_Annotations_SampleAttributesDS.txt

tail -n+2 GTEx_Data_V6_Annotations_SampleAttributesDS.txt \
| cut -f 1,6 \
| sed -e "s/ /_/" \
> SAMPID_to_SMTS.txt

wget http://www.gtexportal.org/static/datasets/gtex_analysis_v6/reference/gencode.v19.genes.patched_contigs.gtf.gz

gunzip -c gencode.v19.genes.patched_contigs.gtf.gz \
| awk '$3=="transcript"' \
| cut -f1,4,5,9 \
| sed -e "s/gene_id \"//" \
| sed -e "s/\".*gene_name \"/\t/" \
| sed -e "s/\".*$//" \
> genes.bed

wget http://www.gtexportal.org/static/datasets/gtex_analysis_v6/rna_seq_data/GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct.gz

gunzip -c GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct.gz \
| python one_per_tissue.py

mv *.bed gtex/.
cd gtex
ls | xargs -P 20 -I {} sh -c "bgzip {}"
cd ..
~/src/giggle/bin/giggle index -i "gtex/*gz" -o gtex_b -f

giggle search -i gtex_b/ \
    -q affected.snps.vcf.gz -o -v \
| python gtex_to_bp.py 10
| python bp.py -o affected_box_plot.png

mkdir data
cd data
wget http://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/all.mnemonics.bedFiles.tgz
tar zxvf all.mnemonics.bedFiles.tgz
cd ..
mkdir split
python rename.py states.txt EDACC_NAME.txt "data/*gz" "split/"
cd split
ls *.bed | xargs -I {} -P 10 sh -c "bgzip {}"
ls *.bed.gz | xargs -I {} -P 10 sh -c "tabix {}"

time ls split/*gz | \
    xargs -I{} \
    sh -c "bedtools intersect -a inkids_rare.bed.gz -b {} | wc -l"

real    2m15.021s
user    1m57.950s
sys 0m16.163s

time ls split/*gz | \
    xargs -I{} \
    sh -c "bedtools intersect -sorted -g genome.txt -a inkids_rare.bed.gz -b {} | wc -l"

real    0m58.092s
user    0m51.030s
sys 0m8.076s

time ls *gz | xargs -I{} tabix {}

real    1m54.741s
user    1m41.347s
sys 0m7.689s

time ls split/*gz | xargs -I{} sh -c "tabix -p bed -B {}  inkids_rare.bed.gz | wc -l"

real    0m26.832s
user    0m19.550s
sys 0m7.597s

time ~/src/giggle/bin/giggle index \
    -i "split/*gz" -o split_i -f
Indexed 55605005 intervals.

real    7m59.121s
user    7m3.515s
sys 0m41.202s

time ~/src/giggle/bin/giggle search -c \
    -q inkids_rare.bed.gz \
    -i split_i 

real    0m0.727s
user    0m0.031s
sys 0m0.677s

time ~/src/giggle/bin/giggle search -s \
    -q inkids_rare.bed.gz \
    -i split_i 

real    0m0.851s
user    0m0.052s
sys 0m0.712s   

time ~/src/giggle/bin/giggle search -v \
    -q inkids_rare.bed.gz \
    -i split_i 

real    0m3.249s
user    0m2.280s
sys 0m0.822s

~/src/giggle/bin/server_overlap \
    1 \
    split_i \
    ~/src/giggle/examples/rme/web/track_names.txt \
    ~/src/giggle/examples/rme/web/header.txt