026fea8dd26483276dbc4d8c860ff0d11e1a640e hiram Thu Jan 23 15:27:43 2020 -0800 now using new minimal makefile with single set of scripts refs #24748 diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl deleted file mode 100755 index 1cfb44d..0000000 --- src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl +++ /dev/null @@ -1,180 +0,0 @@ -#!/usr/bin/env perl - -use strict; -use warnings; -use File::Basename; - -my $topLevel = "/hive/data/genomes/asmHubs"; - -my %betterName; # key is asmId, value is common name -my $hubName = "vertebrate"; -my $Name = "Vertebrate"; -my $srcDocDir = "${hubName}sAsmHub"; - -my $home = $ENV{'HOME'}; -my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; -my $commonNameList = "$hubName.asmId.commonName.tsv"; -my $commonNameOrder = "$hubName.commonName.asmId.orderList.tsv"; - -open (FH, "<$srcDir/${commonNameList}") or die "can not read $srcDir/${commonNameList}"; -while (my $line = <FH>) { - chomp $line; - my ($asmId, $name) = split('\t', $line); - $betterName{$asmId} = $name; -} -close (FH); - -my @orderList; # asmId of the assemblies in order from the *.list files -# the order to read the different .list files: -my $assemblyCount = 0; - -open (FH, "<$srcDir/${commonNameOrder}") or die "can not read ${commonNameOrder}"; -while (my $line = <FH>) { - chomp $line; - my ($commonName, $asmId) = split('\t', $line); - push @orderList, $asmId; - ++$assemblyCount; -} -close (FH); - -my $destDir = "/hive/data/genomes/asmHubs"; - -my $orderKey = 1; -foreach my $asmId (reverse(@orderList)) { - my $accessionDir = substr($asmId, 0 ,3); - $accessionDir .= "/" . substr($asmId, 4 ,3); - $accessionDir .= "/" . substr($asmId, 7 ,3); - $accessionDir .= "/" . substr($asmId, 10 ,3); - $accessionDir .= "/" . $asmId; - $destDir = "/hive/data/genomes/asmHubs/$accessionDir"; - my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir"; - if ( ! -d "${destDir}" ) { - `mkdir -p "${destDir}"`; - } - printf STDERR "ln -s '${buildDir}' '${destDir}'\n"; - `rm -f "${destDir}/bbi"`; - `rm -f "${destDir}/ixIxx"`; - `rm -fr "${destDir}/html"`; - `mkdir -p "${destDir}/html"`; - `rm -f "${destDir}/${asmId}.2bit"`; - `rm -f "${destDir}/${asmId}.agp.gz"`; - `rm -f "${destDir}/${asmId}.chrom.sizes"`; - `rm -f "${destDir}/${asmId}_assembly_report.txt"`; - `rm -f "${destDir}/${asmId}.trackDb.txt"`; - `rm -f "${destDir}/${asmId}.genomes.txt"`; - `rm -f "${destDir}/${asmId}.hub.txt"`; - `rm -f "${destDir}/${asmId}.groups.txt"`; - `ln -s "${buildDir}/bbi" "${destDir}/bbi"`; - `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`; - `ln -s ${buildDir}/html/*.html "${destDir}/html/"`; - my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`; - chomp $jpgFiles; - if ($jpgFiles > 0) { - `rm -f ${destDir}/html/*.jpg`; - `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`; - } -# `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`; - `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/"`; - `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/"`; - `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/"`; -} - -__END__ - -my $hubDir = "/gbdb/hubs/$hubName"; - -`rm -f "${hubDir}/index.html"`; -`ln -s "${destDir}/index.html" "${hubDir}/index.html"`; -`rm -f "${hubDir}/testIndex.html"`; -`ln -s "${destDir}/testIndex.html" "${hubDir}/testIndex.html"`; -`rm -f "${hubDir}/testAsmStats${Name}.html"`; -`ln -s "${destDir}/testAsmStats${Name}.html" "${hubDir}/testAsmStats${Name}.html"`; - -__END__ -; - my $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; - my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`; - chomp $descr; - my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`; - chomp $orgName; - $orgName = $betterName{$asmId} if (exists($betterName{$asmId})); - - printf "genome %s\n", $asmId; - printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId; - printf "groups groups.txt\n"; - printf "description %s\n", $orgName; - printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId; - printf "organism %s\n", $descr; - my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`; - chomp $chrName; - my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`; - chomp $bigChrom; - my $oneThird = int($bigChrom/3); - my $tenK = $oneThird + 10000; - $tenK = $bigChrom if ($tenK > $bigChrom); - my $defPos="${chrName}:${oneThird}-${tenK}"; - if ( -s "$asmId/defaultPos.txt" ) { - $defPos=`cat "$asmId/defaultPos.txt"`; - chomp $defPos; - } - printf "defaultPos %s\n", $defPos; - printf "orderKey %d\n", $orderKey++; - printf "scientificName %s\n", $descr; - printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId; - printf "\n"; - my $localGenomesFile = "$buildDir/${asmId}.genomes.txt"; - open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile"; - printf GF "genome %s\n", $asmId; - printf GF "trackDb %s/%s.trackDb.txt\n", $asmId, $asmId; - printf GF "groups groups.txt\n"; - printf GF "description %s\n", $orgName; - printf GF "twoBitPath %s/%s.2bit\n", $asmId, $asmId; - printf GF "organism %s\n", $descr; - printf GF "defaultPos %s\n", $defPos; - printf GF "orderKey %d\n", $orderKey++; - printf GF "scientificName %s\n", $descr; - printf GF "htmlPath %s/html/%s.description.html\n", $asmId, $asmId; - close (GF); -} - -__END__ - -description Mastacembelus armatus -twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit -organism Zig-Zag eel -defaultPos LR535842.1:14552035-14572034 -orderKey 1 -scientificName Mastacembelus armatus -htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html - -# head -25 GCA_002180035.3_HG00514_prelim_3.0_assembly_report.txt - -# Assembly name: HG00514_prelim_3.0 -# Organism name: Homo sapiens (human) -# Isolate: HG00514 -# Sex: female -# Taxid: 9606 -# BioSample: SAMN04229552 -# BioProject: PRJNA300843 -# Submitter: The Genome Institute at Washington University School of Medicine -# Date: 2018-05-22 -# Assembly type: haploid -# Release type: major -# Assembly level: Chromosome -# Genome representation: full -# WGS project: NIOH01 -# Assembly method: Falcon v. November 2016 -# Expected final version: no -# Genome coverage: 80.0x -# Sequencing technology: PacBio RSII -# GenBank assembly accession: GCA_002180035.3 -# -## Assembly-Units: -## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name -## GCA_002180045.3 Primary Assembly -