05a3d177bf35df451f750276c274efc25b8acc70
markd
  Fri May 13 14:28:34 2022 -0700
import of gencode VM30 pre-release

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 132b97e..27924dc 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -5,31 +5,31 @@
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM26
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M26 103 'Feb 2021'
 
     # If being pushed public, update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM26.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
@@ -46,31 +46,31 @@
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM27
     pushd /hive/data/genomes/mm39/bed/gencodeVM27
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M27 104 'May 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM27.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM27
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
@@ -83,31 +83,31 @@
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M28 105 'Oct 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImportPre.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
@@ -120,31 +120,31 @@
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
 
     (time nice make -kO -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M28 105 'Oct 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
@@ -157,59 +157,86 @@
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M29 106 'Feb 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM29/hgcImportPre.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
 2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 release (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M29 106 'Feb 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
-    # edit human/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM29/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
+2022-05-13: import of UCSC GENCODE group processing of GENCODE VM30 pre-release (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
+    pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
+
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M30 107 'June 2022'
+
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include  as alpha
+    jkmake DBS=mm39
+
+    # edit all.joiner to add ~/tmp/gencodeVM30.joiner
+
+    pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=mm39 alpha
+##############################################################################