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Peter Kerpedjiev edited this page Jan 30, 2017 · 31 revisions

Gene annotations

Many

aws s3 sync s3://pkerp/public/hg-server/data/hg19 \
    /data/tmp \
    --exclude '*' \
    --include '*multires.cool'

for file in $(ls /data/tmp/hg19/*.multires.cool);
   do

   curl -F "datafile=@${file}" \
    -F "filetype=cooler" \
    -F "datatype=matrix" \
    -F "coordSystem=hg19" \
    http://localhost:80/api/v1/tilesets/
done;

Gene annotations

ASSEMBLY=hg19
curl -X "DELETE" localhost:80/tilesets/dd/

FILE=gene-annotations-${ASSEMBLY}.db
rm /tmp/$FILE
wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/${FILE}
curl -F "datafile=@/tmp/gene-annotations-${ASSEMBLY}.db" \
     -F "filetype=beddb" \
     -F "datatype=gene-annotation" \
     -F "uid=dd" \
     -F "name=Gene Annotations" \
     -F "coordSystem=${ASSEMBLY}" \
     localhost:80/tilesets/

HiCCUPs (Rao et al. 2014, GSE63525_GM12878_primary+replicate)

curl -X "DELETE" localhost:80/tilesets/i/

wget -N -P /tmp/ \
     https://s3.amazonaws.com/pkerp/public/hg-server/data/GSE63525_GM12878_primary%2Breplicate_HiCCUPS_looplist.txt.gz.multires.db

curl -F "datafile=@/tmp/GSE63525_GM12878_primary+replicate_HiCCUPS_looplist.txt.gz.multires.db" \
     -F "filetype=bed2ddb" \
     -F "datatype=hiccups-loops" \
     -F name="HiCCUPs Loops (Rao et al. 2014, GM12878 primary + replicate)" \
     -F "uid=i" \
     -F "coordSystem=hg19" \
    http://localhost:80/tilesets/

Arrowhead Domains (Rao et al. 2014, GSE63525_GM12878_primary+replicate)

wget -N -P /tmp/ \
     https://s3.amazonaws.com/pkerp/public/hg-server/data/GSE63525_GM12878_primary%2Breplicate_Arrowhead_domainlist.txt.gz.multires.db

curl -F "datafile=@/tmp/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt.gz.multires.db" \
     -F "filetype=bed2ddb" \
     -F "datatype=arrowhead-domains" \
     -F"name=Arrowhead domains (Rao et al. 2014, GM12878 primary + replicate)" \
     -F "uid=f" \
     -F "coordSystem=hg19" \
    http://localhost:80/tilesets/

ENCODE CTCF

curl -X "DELETE" localhost:80/tilesets/a1/

wget -N -P /tmp/ \
    https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig.hitile

curl -F "datafile=@/tmp/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig.hitile" \
    -F "filetype=hitile" \
    -F "datatype=vector" \
    -F "uid=a1" \
    -F "coordSystem=hg19" \
    -F "name=CTCF GM12878 Std Sig" \
    http://localhost:80/tilesets/

Caltech RNASeq

curl -X "DELETE" localhost:80/tilesets/bb/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile
curl -F "datafile=@/tmp/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile" \
    -F "filetype=hitile" \
    -F "datatype=vector" \
    -F "uid=bb" \
    -F "coordSystem=hg19" \
    http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Dixon2015-H1_TB-HindIII-allreps-filtered.10kb.multires.cool
curl -F "datafile=@/tmp/Dixon2015-H1_TB-HindIII-allreps-filtered.10kb.multires.cool" \
    -F "filetype=cooler" \
    -F "datatype=matrix" \
    -F "uid=aa" \
    -F "coordSystem=hg19" \
    http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Dixon2015-H1_TB-HindIII-allreps-filtered.10kb.multires.cool
curl -F "datafile=@/tmp/Dixon2015-H1_TB-HindIII-allreps-filtered.10kb.multires.cool" \
    -F "filetype=cooler" \
    -F "datatype=matrix" \
    -F "uid=aa" \
    -F "coordSystem=hg19" \
    http://localhost:80/tilesets/

Dixon2012-H1hESC-HindII 1Kb

wget -N -P /tmp/ \
https://s3.amazonaws.com/pkerp/public/hg-server/data/Dixon2012-H1hESC-HindIII-allreps-filtered.1kb.multires.cool

curl -F "datafile=@/tmp/Dixon2012-H1hESC-HindIII-allreps-filtered.1kb.multires.cool" \
    -F "filetype=cooler" \
    -F "datatype=matrix" \
    -F "coordSystem=hg19" \
    http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/
https://s3.amazonaws.com/pkerp/public/hg-server/data/Dixon2012-H1hESC-HindIII-allreps-filtered.1kb.multires.cool

curl -F "datafile=@/tmp/Dixon2012-H1hESC-HindIII-allreps-filtered.1kb.multires.cool"
-F "filetype=cooler"
-F "datatype=matrix"
-F "coordSystem=hg19"
http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Rao2014-GM12878-MboI-allreps-filtered.10kb.multires.cool curl -F "datafile=@/tmp/Rao2014-GM12878-MboI-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" -F "coordSystem=gh19" http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Rao2014-HMEC-MboI-allreps-filtered.10kb.multires.cool curl -F "datafile=@/tmp/Rao2014-HMEC-MboI-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" -F "coordSystem=hg19" http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Rao2014-HUVEC-MboI-allreps-filtered.10kb.multires.cool curl -F "datafile=@/tmp/Rao2014-HUVEC-MboI-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" -F "coordSystem=hg19" http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Rao2014-IMR90-MboI-allreps-filtered.10kb.multires.cool curl -F "datafile=@/tmp/Rao2014-IMR90-MboI-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" -F "coordSystem=hg19" http://localhost:80/api/v1/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Rao2014-K562-MboI-allreps-filtered.10kb.multires.cool curl -F "datafile=@/tmp/Rao2014-K562-MboI-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" -F "coordSystem=hg19" http://localhost:80/api/v1/tilesets/


wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/Dixon2015-H1_MS-HindIII-allreps-filtered.10kb.multires.cool
curl -F "datafile=@/tmp/Dixon2015-H1_MS-HindIII-allreps-filtered.10kb.multires.cool" -F "filetype=cooler" -F "datatype=matrix" http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeSydhTfbsGm12878InputStdSig.hitile
curl -F "datafile=@/tmp/wgEncodeSydhTfbsGm12878InputStdSig.hitile" -F "filetype=hitile" -F "datatype=vector" http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeSydhTfbsGm12878Pol2s2IggmusSig.hitile
curl -F "datafile=@/tmp/wgEncodeSydhTfbsGm12878Pol2s2IggmusSig.hitile" -F "filetype=hitile" -F "datatype=vector" http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig.hitile
curl -F "datafile=@/tmp/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig.hitile" -F "filetype=hitile" -F "datatype=vector" http://localhost:80/tilesets/

wget -N -P /tmp/ https://s3.amazonaws.com/pkerp/public/hg-server/data/wgEncodeSydhTfbsGm12878Rad21IggrabSig.hitile
curl -F "datafile=@/tmp/wgEncodeSydhTfbsGm12878Rad21IggrabSig.hitile" -F "filetype=hitile" -F "datatype=vector" http://localhost:80/tilesets/
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