0a6421e764888bb6e8e1b2058501f7ce4188d814
markd
  Mon Jun 17 02:08:53 2019 -0700
import of prerelease of gencode V31lift37

diff --git src/hg/makeDb/doc/transMapTracks.txt src/hg/makeDb/doc/transMapTracks.txt
index 3505500..5a37e5c 100644
--- src/hg/makeDb/doc/transMapTracks.txt
+++ src/hg/makeDb/doc/transMapTracks.txt
@@ -86,15 +86,53 @@
 
   # add trackDb entries at top level by editing:
     src/hg/makeDb/trackDb/trackDb.transMap.ra 
   # create push lists for databases and gbdb files for genomes on hgwbeta:
     ${tmdir}/bin/mkPushList ${tmdir}/etc/transMapBuildConf.py db.push.lst gbdb.push.lst
 
   # and creating the following html files:
     transMapV4.html
     transMapEnsemblV4.html
     transMapEstV4.html
     transMapRefseqV4.html
     transMapRnaV4.html
 
 
 ##############################################################################################
+# TransMap V5 tracks (2019-06-10 markd)
+##
+  - Build code is here:
+       /cluster/home/markd/compbio/repos/git/transMap.git
+    which also requires
+      /cluster/home/markd/compbio/repos/git/pycbio.git
+      git@github.com:diekhans/pipettor.git
+
+  - Build process:
+    # IMPORTANT: SET VERSION IN transMap-dev/etc/transMapBuildConf.py
+    tmdir=~/compbio/projs/transMap/transMap-dev
+    mkdir -p  /hive/data/inside/transMap/V5/logs
+    pushd /hive/data/inside/transMap/V5
+    (time nice ${tmdir}/bin/luigiTransMap --workers=32 --logConfFile=${tmdir}/etc/logging.conf ${tmdir}/etc/transMapBuildConf.py) >&logs/2019-06-10.log &
+    # takes maybe 10-14 hours,  at the end, check for parasol jobs
+    # that are lost (using one or two stranglers for a few batches), then do
+    para stop -batch=/the/batch/name
+    para push -batch=/the/batch/name
+    # now wait for luigiTransMap to complete.  Must manually check log, as
+    # current luigi doesn't exit non-zero if there were errors
+
+  # create symlinks to /gbdb for bigPsl files
+    ${tmdir}/bin/linkToGbdb  ${tmdir}/etc/transMapBuildConf.py
+
+  # add trackDb entries at top level by editing:
+    src/hg/makeDb/trackDb/trackDb.transMap.ra 
+  # create push lists for databases and gbdb files for genomes on hgwbeta:
+    ${tmdir}/bin/mkPushList ${tmdir}/etc/transMapBuildConf.py db.push.lst gbdb.push.lst
+
+  # and creating the following html files:
+    transMapV5.html
+    transMapEnsemblV5.html
+    transMapEstV5.html
+    transMapRefseqV5.html
+    transMapRnaV5.html
+
+
+##############################################################################################