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
@@ -1,100 +1,138 @@
 
 TransMap maps transcripts from source assemblies to destination assemblies via chains.
 
 Tracks are built across current vertebrate assemblies concurrently.  The
 concurrent build is done as the fasta files and metadata tables for the source
 transcripts are shared and stored in hgFixed/gbdb.  Modifications will be
 made to allow incrementally add destination genomes.
 
 TransMap build is based on the pslMap and other tools in the kent/src tree.
 The driver for generating the data is available in
  
    hg clone /cluster/home/markd/compbio/repos/hg/transMap
 it also requires
    hg clone /cluster/home/markd/compbio/repos/hg/pycbio
 
 The source is checkout and run in
     /hive/data/inside/transMap/build
 
 General steps for setup, only done once:
 
     cd /hive/data/inside/transMap/build
     hg clone /cluster/home/markd/compbio/repos/hg/transMap
     mkdir transMap/extern
     cd  transMap/extern
     hg clone /cluster/home/markd/compbio/repos/hg/pycbio
     (cd pycbio && make)
 
 ##############################################################################################
 # TransMap V3 tracks (2014-12-18 markd)
 ##
    # get data and setup batch
    make getData
    make batchSetup
 
    # build mappings
    ssk kk
    para create -batch=para1/aln para1/aln/jobs.para
    para try -batch=para1/aln
    para push -batch=para1/aln -maxPush=1000000
    para create -batch=para1/filt para1/filt/jobs.para
    para try -batch=para1/filt
    para push -batch=para1/filt -maxPush=1000000
 
    # load and verify data
    ssh hgwdev
    make -j 8 loadDb
    make runJoinerCheck
 
    # create push.list which has all tables for databases active on RR or hgwbeta
    make pushList
 
    # create template for hg/makeDb/doc that points to this file and append it to all
    # database in this build:
    destDbs=$(make printDestDbs)
    cd ~kent/src/hg/makeDb/doc
    for db in $destDbs ; do cat /hive/data/inside/transMap/build/transMap/builds/vertebrate.2014-12-11.V3/makedb.doc.template >> $db.txt; done
 
 
    # request push of tracks
    # note: was never made public
 ##############################################################################################
 # TransMap V4 tracks (2017-02-10 markd)
 ##
   - This is the build using bigTransMap format (derived from bigPsl), not
     mysql tracks.
     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:
     tmdir=~/compbio/projs/transMap/transMap-dev
     mkdir -p  /hive/data/outside/transMap/V4/logs
     pushd /hive/data/outside/transMap/V4
     (time nice ${tmdir}/bin/luigiTransMap --workers=32 --logConfFile=${tmdir}/etc/logging.conf ${tmdir}/etc/transMapBuildConf.py) >&logs/2017-01-12.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:
     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
+
+
+##############################################################################################