an interactive Hi-C data visualizer. galaxy/higlass-it:1.0 80 $__history_id__ $__galaxy_url__ 8080 $__galaxy_url__ > uploaded.txt && ## Lists all genomes being used that haven't been uploaded, checks if they are in the negspy directory, creates chromsize info if so #for $count, $input in enumerate($inputs): #for $file in $input.fileselect.inputfiles: #if $file.metadata.dbkey in $existing_genomes: echo $file.metadata.dbkey >> datatypes.txt && #end if #end for #end for sort datatypes.txt | uniq | sed 's/^?//' > types.txt && cat types.txt | while read datatypes; do genome="negspy/negspy/data/"\$datatypes"/chromInfo.txt"; python higlass-server/manage.py ingest_tileset --filename \$genome --filetype chromsizes-tsv --datatype chromsizes --coordSystem \$datatypes; done; ## Full dataset uploads #for $count, $input in enumerate($inputs): #if $input.fileselect.typeselect == "bed": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier + "." + str($file.ext) cp $file $filename && clodius aggregate bedfile --assembly $file.metadata.dbkey $filename && mv ${filename}.beddb data/${file.element_identifier} && python higlass-server/manage.py ingest_tileset --filename data/${file.element_identifier} --filetype beddb --datatype bedlike --coordSystem $file.metadata.dbkey && #end for #elif $input.fileselect.typeselect == "bigwig": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier cp $file $filename && python higlass-server/manage.py ingest_tileset --filename ${filename} --filetype bigwig --datatype vector --coordSystem ${file.metadata.dbkey} && #end for #elif $input.fileselect.typeselect == "bedgraph": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier + "." + str($file.ext) cp $file $filename && cat $filename | sort -k1,1 -k2,2n | awk '{ if (NF >= 4) print $${file.metadata.chromCol} "\t" $${file.metadata.startCol} "\t" $${file.metadata.endCol} "\t" $${input.fileselect.valuecol}}' > ${filename}.presort; #if $file.metadata.dbkey in $existing_genomes: bedGraphToBigWig ${filename}.presort negspy/negspy/data/${file.metadata.dbkey}/chromInfo.txt ${filename}.bigwig && #else bedGraphToBigWig ${filename}.presort $uploaded_genomes[str($file.metadata.dbkey)] ${filename}.bigwig && #end if mv ${filename}.bigwig data/${file.element_identifier} && python higlass-server/manage.py ingest_tileset --filename data/${file.element_identifier} --filetype bigwig --datatype vector --coordSystem ${file.metadata.dbkey} && #end for #elif $input.fileselect.typeselect == "bigbed": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier + "." + str($file.ext) cp $file $filename && bigBedToBed ${filename} ${file.element_identifier} && clodius aggregate bedfile --assembly $file.metadata.dbkey ${file.element_identifier} && mv ${file.element_identifier}.beddb data/${file.element_identifier} && python higlass-server/manage.py ingest_tileset --filename data/${file.element_identifier} --filetype beddb --datatype bedlike --coordSystem $file.metadata.dbkey && #end for #elif $input.fileselect.typeselect == "mcool": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier cp $file $filename && python higlass-server/manage.py ingest_tileset --filename $filename --filetype cooler --datatype matrix && #end for #elif $input.fileselect.typeselect == "cool": #for $file in $input.fileselect.inputfiles: #set $filename = "data/" + $file.element_identifier + "." + str($file.ext) cp $file $filename && cooler zoomify -r $input.fileselect.zoomval -o data/${file.element_identifier} $filename && ###if $input.fileselect.granularity == "Yes": ## cooler zoomify -r $input.fileselect.granularity.zoomval -o data/${file.element_identifier}.mcool $filename && ###else: ## cooler coarsen -k $input.fileselect.granularity.binsize -o data/${file.element_identifier}.mcool $filename ###end if python higlass-server/manage.py ingest_tileset --filename data/${file.element_identifier} --filetype cooler --datatype matrix && #end for #end if #end for tail -f /var/log/supervisor/* ]]> **Note: This interactive tool is in alpha. There is a known bug in the source tool that fails to render the image of the viewport on uploaded data. Further, uploaded coordinate file loaded in will have the same name in the in-app file select.** Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions. For a detailed documentaition please visit https://docs.higlass.io/. **All files must have an associated genome assembly** **Please be patient during startup, files will become available in higlass as they finish loading.** ================================================================================================================== Available genonmes/assemblies: GCA_000001215.4_Release_6_plus_ISO1_MT_genomic, GCF_000005845.2_ASM584v2_genomic, canFam3, danRer10, dm6, galGal6, grch37, h37rv, hg19, hs37d5, mm9, panTro5, rn6, GCA_000001405.15_GRCh38_genomic, b37, ce11, dm3, galGal5, gorGor5, grch37-lite, hg18, hg38, mm10, mm9b, rheMac8, sacCer3, test3chroms ================================================================================================================== **If your genome/assembly is not listed, please upload a chromosome size file in the following format:** ============================== chr1 chr1_size chr2 chr2_size ... ============================== 10.1186/s13059-018-1486-1