adea08b7a8578f96a2e819466754b24ad79645f6 max Mon Oct 3 13:27:41 2022 -0700 removing old panelApp makedoc, refs #25568 diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt index 3e3eaaf..d7eee3d 100644 --- src/hg/makeDb/doc/hg38/hg38.txt +++ src/hg/makeDb/doc/hg38/hg38.txt @@ -6960,56 +6960,30 @@ #real 9m31.900s #user 9m1.624s #sys 0m20.863s hgLoadChain hg38 -tIndex chainHg19ReMap remap.hg38.hg19.chain #Loading 5315 chains into hg38.chainHg19ReMap time axtChain -psl -linearGap=medium -verbose=0 remap.hg38.hg19.psl \ /hive/data/genomes/hg38/hg38.2bit /hive/data/genomes/hg19/hg19.2bit \ remap.axtChain.hg38.hg19.chain #real 2m26.333s #user 2m4.237s #sys 0m22.071s hgLoadChain hg38 -tIndex chainHg19ReMapAxtChain remap.axtChain.hg38.hg19.chain #Loading 2115 chains into hg38.chainHg19ReMapAxtChain ################################################### - -# PanelApp refs #25568 -cd /hive/data/genomes/hg38/bed -mkdir panelApp -cd panelApp -wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/panel_hg38.bb -wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/str_hg38.bb -mv /cluster/home/bnguy/trackhub/region/region_hg38.bb . -mv panel_hg38.bb genesPanel.bb -mv str_hg38.bb STRsPanel.bb -mv region_hg38.bb CNVregions.bb -cd /gbdb/hg38 -mkdir panelApp -cd panelApp -ln -s /hive/data/genomes/hg38/bed/panelApp/genesPanel.bb -ln -s /hive/data/genomes/hg38/bed/panelApp/STRsPanel.bb -ln -s /hive/data/genomes/hg38/bed/panelApp/CNVregions.bb -cd ~/kent/src/hg/makeDb/trackDb/human/hg38 -wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/panelapp.html -mv panelapp.html panelApp.html -curl https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/trackDb.txt >> trackDb.ra -vi trackDb.ra -cd ~/kent/src/hg/makeDb/trackDb -make alpha DBS=hg38 - -###### #Agilent SNP/CNV arrays 3/11/21 #Downloaded by web browser cd /hive/data/genomes/hg38/bed/agilentProbes/genetiSureCyto fetchChromSizes hg38 > hg38.chrom.sizes bedSort hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed uniq hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed >hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.uniq.bed bedToBigBed hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.uniq.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bb bedSort hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed uniq hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed > hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.uniq.bed bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.uniq.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bb bedSort hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed uniq hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed > hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.uniq.bed bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.uniq.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bb mkdir -p /gbdb/hg38/snpCnvArrays/agilent cd /gbdb/hg38/snpCnvArrays/agilent