40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e
max
  Tue Feb 6 07:05:20 2024 -0800
documenting the online/offline and dev options in GBIC, no ticket

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index c076eb0..0318ce6 100644
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -358,41 +358,50 @@
 
 cramRef=$APACHEDIR/userdata/cramCache
 
 EOF_HGCONF
 
 read -r -d '' HELP_STR << EOF_HELP
 $0 [options] [command] [assemblyList] - UCSC genome browser install script
 
 command is one of:
   install    - install the genome browser on this machine. This is usually 
                required before any other commands are run.
   minimal    - download only a minimal set of tables. Missing tables are
                downloaded on-the-fly from UCSC.
   mirror     - download a full assembly (also see the -t option below).
                After completion, no data is downloaded on-the-fly from UCSC.
+  offline    - put the browser offline, so no more loading of missing tables
+               from UCSC on-the-fly. Much faster, but depending on how much
+               you downloaded, means that you have many fewer tracks available.
+  online     - put the browser online, so any missing files and tracks are
+               loaded on-the-fly from UCSC.
   update     - update the genome browser software and data, updates
                all tables of an assembly, like "mirror"
   cgiUpdate  - update only the genome browser software, not the data. Not 
                recommended, see documentation.
   clean      - remove temporary files of the genome browser older than one 
                day, but do not delete any uploaded custom tracks
   addTools   - copy the UCSC User Tools, e.g. blat, featureBits, overlapSelect,
                bedToBigBed, pslCDnaFilter, twoBitToFa, gff3ToGenePred, 
                bedSort, ... to /usr/local/bin
                This has to be run after the browser has been installed, other-
                wise these packages may be missing: libpng zlib libmysqlclient
+  dev        - install git/gcc/c++/freetype/etc, clone the kent repo into
+               ~/kent and build the CGIs into /usr/local/apache so you can try
+               them right away. Useful if you want to develop your own track 
+               types.
   mysql      - Patch my.cnf and recreate Mysql users. This can fix
                a broken Mysql server after an update to Mysql 8. 
                
 
 parameters for 'minimal', 'mirror' and 'update':
   <assemblyList>     - download Mysql + /gbdb files for a space-separated
                        list of genomes
 
 examples:
   bash $0 install     - install Genome Browser, do not download any genome
                         assembly, switch to on-the-fly mode (see the -f option)
   bash $0 minimal hg19 - download only the minimal tables for the hg19 assembly
   bash $0 mirror hg19 mm9 - download hg19 and mm9, switch
                         to offline mode (see the -o option)
   bash $0 -t noEncode mirror hg19  - install Genome Browser, download hg19 
@@ -2135,23 +2144,29 @@
 elif [ "${1:-}" == "cgiUpdate" ]; then
    cgiUpdate
 
 elif [ "${1:-}" == "update" ]; then 
    updateBrowser ${@:2} # all arguments after the second one
 
 elif [ "${1:-}" == "clean" ]; then
     cleanTrash
 
 elif [ "${1:-}" == "addTools" ]; then
     addTools
 
 elif [ "${1:-}" == "mysql" ]; then
     mysqlDbSetup
 
+elif [ "${1:-}" == "online" ]; then
+    goOnline
+
+elif [ "${1:-}" == "offline" ]; then
+    goOffline
+
 elif [ "${1:-}" == "dev" ]; then
     buildTree 
 
 else
-   echo Unknown command: $1
+   echo Unknown command: ${1:-}
    echo "$HELP_STR"
    exit 100
 fi