e254083e7f7e36e3d4ddc2324dbe622b8407a887
chmalee
  Mon Apr 24 14:21:27 2023 -0700
Have GBiC automatically make the cram cache directories on install, refs Lon email

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index 242fd2a..adedaff 100644
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -342,30 +342,32 @@
 # Programs required for per-SNP geographic maps of HGDP population
 # allele frequencies:
 hgc.psxyPath=/usr/lib/gmt/bin/psxy
 hgc.ps2rasterPath=/usr/lib/gmt/bin/ps2raster
 hgc.ghostscriptPath=/usr/bin/ghostscript
 
 # legacy setting
 browser.indelOptions=on
 # sql debugging: uncomment to see all SQL commands in the apache log
 #JKSQL_TRACE=on
 #JKSQL_PROF=on
 
 freeType=on
 freeTypeDir=../htdocs/urw-fonts
 
+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.
   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 
@@ -1421,30 +1423,34 @@
             exit 100
         fi
     fi
 
     # check if /usr/local/apache is empty
     # on OSX, we had to create an empty htdocs, so skip this check there
     if [ -d "$APACHEDIR" -a "$OS" != "OSX" ]; then
         echo2 error: the directory $APACHEDIR already exists.
         echo2 This installer has to overwrite it, so please move it to a different name
         echo2 or remove it. Then start the installer again with "bash $0 install"
         exit 100
     fi
 
     mysqlDbSetup
 
+    # setup the cram cache so remote cram files will load correctly
+    mkdir -p $APACHEDIR/userdata/cramCache/{error,pending}
+    chmod -R 777 $APACHEDIR/userdata/cramCache
+
     # -------------------
     # CGI installation
     # -------------------
     echo2
     echo2 Creating $CGIBINDIR and $HTDOCDIR and downloading contents from UCSC
     waitKey
     
     # create apache directories: HTML files, CGIs, temporary and custom track files
     mkdir -p $HTDOCDIR $CGIBINDIR $TRASHDIR $TRASHDIR/customTrash
     
     # the CGIs create links to images in /trash which need to be accessible from htdocs
     cd $HTDOCDIR
     ln -fs $TRASHDIR
     
     # write the sample hg.conf ti the cgi-bin directory