2574b18caca333a5d52d6d6b8ecc6424d403c7d7
galt
  Tue Oct 5 22:01:49 2021 -0700
more p13 made properly versioned gc5Base files for top, intial, p12, p13, latest bigZips doownloads dirs. refs #25091

diff --git src/hg/makeDb/doc/hg38/patchUpdate.13.txt src/hg/makeDb/doc/hg38/patchUpdate.13.txt
index f23a669..f101205 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.13.txt
@@ -152,30 +152,107 @@
     rm md5sum.txt
     md5sum hg38* > md5sum.txt
     echo GRCh38.p13 > LATEST_VERSION
 
     rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p13
     ln -s /hive/data/genomes/hg38/goldenPath/bigZips/p13 \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p13
     rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
     ln -s /hive/data/genomes/hg38/goldenPath/bigZips/latest \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
     ln -sf /hive/data/genomes/hg38/chrom.sizes.p13 \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p13/hg38.p13.chrom.sizes
 
 
 #############################################################################
+# Put correct gc5Base files in downloads (DONE 2021-10-05 galt)
+# I found that there were nice versioned files made by the patch process,
+# but that they had never been correctly used, and in fact, the lastest one w
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/initial
+
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.initial.gc5Base.bw hg38.gc5Base.bw
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.initial.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
+
+md5sum hg38.* > md5sum.txt
+diff md5sum.txt md5sum.txt2
+md5sum hg38.* > md5sum.txt2
+rm md5ssum.txt2
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips
+ln -s initial/hg38.chrom.sizes hg38.chrom.sizes 
+ln -s initial/hg38.gc5Base.bw hg38.gc5Base.bw
+ln -s initial/hg38.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/p11
+
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p11.gc5Base.bw hg38.p11.gc5Base.bw
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p11.gc5Base.wigVarStep.gz hg38.p11.gc5Base.wigVarStep.gz
+ln -s /hive/data/genomes/hg38/chrom.sizes.p11 hg38.p11.chrom.sizes
+
+md5sum hg38.p11.gc5Base.* >> md5sum.txt2
+diff md5sum.txt md5sum.txt2
+md5sum hg38.* > md5sum.txt2
+rm md5ssum.txt2
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/p12
+
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p12.gc5Base.bw hg38.p12.gc5Base.bw
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p12.gc5Base.wigVarStep.gz hg38.p12.gc5Base.wigVarStep.gz
+
+md5sum hg38.p12.gc5Base.* >> md5sum.txt
+
+md5sum hg38.* > md5sum.txt2
+diff md5sum.txt md5sum.txt2
+rm md5sum.txt2
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/p13
+
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p13.gc5Base.bw hg38.p13.gc5Base.bw
+ln -s /hive/data/genomes/hg38/bed/gc5Base/hg38.p13.gc5Base.wigVarStep.gz hg38.p13.gc5Base.wigVarStep.gz
+
+md5sum hg38.p13.gc5Base.* >> md5sum.txt
+
+md5sum hg38.* > md5sum.txt2
+diff md5sum.txt md5sum.txt2
+rm md5sum.txt2
+
+cd /hive/data/genomes/hg38/goldenPath/bigZips/latest
+
+ln -s ../p13/hg38.p13.chrom.sizes hg38.chrom.sizes
+
+ln -s ../p13/hg38.p13.gc5Base.bw hg38.gc5Base.bw
+ln -s ../p13/hg38.p13.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
+
+md5sum hg38.* > md5sum.txt2
+
+sed -e 's/.p13//' ../p13/md5sum.txt > md5sum.p13
+
+diff md5sum.p13 md5sum.txt2
+rm md5sum.p13
+rm md5sum.txt2
+
+-
+
+cd /data/apache/htdocs-hgdownload/goldenPath/hg38/bigZips
+rm hg38.chrom.sizes
+ln -s /hive/data/genomes/hg38/goldenPath/bigZips/hg38.chrom.sizes hg38.chrom.sizes
+ln -s /hive/data/genomes/hg38/goldenPath/bigZips/hg38.gc5Base.bw hg38.gc5Base.bw
+ln -s /hive/data/genomes/hg38/goldenPath/bigZips/hg38.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
+
+
+#############################################################################
 # Build perSeqMax file for gfServer (hgBlat) (DONE 2021-08-26 galt)
     # When the blat server is restarted with the updated hg38.2bit file,
     # hg38.altsAndFixes needs to be copied over along with the new hg38.2bit file,
     # and gfServer needs to be restarted with -perSeqMax=hg38.altsAndFixes.
     cd /hive/data/genomes/hg38
     cut -f 1 chrom.sizes.p13 \
     | grep -E '_(alt|fix)$' \
     | sed -re 's/^/hg38.2bit:/;' \
       > hg38.altsAndFixes.p13
     # Link for blat server installation convenience:
     ln -sf hg38.altsAndFixes.p13 altsAndFixes
 
 
 #########################################################################
 # Regenerate idKeys with extended hg38 (DONE 2021-08-26 galt)
@@ -327,32 +404,34 @@
   ok="OK"
   if [ "$c0" -ne "$c1" ]; then
      ok="ERROR"
   fi
   printf "# checking $t: $c0 =? $c1 $ok\n"
 done
 # checking refseq: 639 =? 639 OK
 # checking genbank: 640 =? 640 OK
 # checking assembly: 640 =? 640 OK
     # Note how there's one fewer refseq, consistent with featureBits above.
 
     hgLoadSqlTab hg38 chromAlias $HOME/kent/src/hg/lib/chromAlias.sql ${db}.chromAlias.tab
 
 
 ##############################################################################
-# UCSC to Ensembl (TODO 2020-08-10 galt)
-# doc??
+# UCSC to Ensembl (TODO 2021-09-18 galt)
+# Ask Hiram to update ensembleToUcsc and ensemblLift tables.
+# FYI ensemblLift offset shows how many Ns were inserted by Ensembl to give the right coordinate to alts and fixes.
+#
 
 
 ############################################################################
 # altLocations and patchLocations (DONE 2021-08-27 galt)
     # indicate corresponding locations between haplotypes and reference
     mkdir /hive/data/genomes/hg38/bed/altLocations.p13
     cd /hive/data/genomes/hg38/bed/altLocations.p13
     ~/kent/src/hg/utils/automation/altScaffoldPlacementToBed.pl \
       /hive/data/genomes/grcH38P13/genbank/GCA_000001405.28_GRCh38.p13_assembly_structure/{ALT_*,PATCHES}/alt_scaffolds/alt_scaffold_placement.txt \
     | sort -k1,1 -k2n,2n \
       > altAndFixLocations.bed
     wc -l altAndFixLocations.bed
 #892 altAndFixLocations.bed
     grep _alt altAndFixLocations.bed > altLocations.bed
     grep _fix altAndFixLocations.bed > fixLocations.bed