178eda0f816c2044f1e5f4a87aa890c4c2c115d9
kent
  Tue Oct 1 20:08:43 2024 -0700
Seperating out the user initialization into a script and adding groups to it too.

diff --git src/hg/cirm/cdw/install/README src/hg/cirm/cdw/install/README
index 5fbcadf..353c660 100644
--- src/hg/cirm/cdw/install/README
+++ src/hg/cirm/cdw/install/README
@@ -1,86 +1,84 @@
 Installation overview for Cell Data Warehouse (CDW).
 
 1) First bring up a recent linux distribution.
 2) Run a Genome Browser Install script that should include mysql/mariaDb install.
 3) Add in (with dnf install) libpng-devel, libuuid-devel, mariadb-devel, nodejs
 4) Create a cdw user at the Unix level that will be the one to run the daemons.
 5) Create the following directories and make them writable and executable by
    the cdw user.
    	$HOME/cdw/bin/scripts
 	$HOME/cdw/bin/x86_64
 	$HOME/cdw/backups
 	/usr/local/apache/cgi-bin-cdw
    Also set up the environmental variable CIRM to point to $HOME/cdw
 6) Log in as the cdw user
 7) Get the Kent UCSC source and execute the following makes from the 
    src directory:
        cd ~/kent/src
        make -j 16 libs
        cd ~/kent/src/hg/cirm/cdw
        make -j 16
        cd ~/kent/src/tagStorm
        make -j 16
        cd ~/kent/src/hg/hgsql
        make
        cd ~/kent/src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats
        make
        cd ~/kent/src/hg/encode3/encodeDataWarehouse/utils/edwBamStats
        make
        cd ~/kent/src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis
        make
        cd ~/kent/src/utils/fastqStatsAndSubsample
        make
        cd ~/kent/src/utils/bigBedToBed
        make
        cd ~/kent/src/utils/bigWigAverageOverBed
        make
 8) Make up a configuration file for accessing the database in ~/.hg.conf
     with the following six lines:
        db.host=localhost
        db.user=cdw
        db.password=
        cdw.host=localhost
        cdw.user=cdw
        cdw.password=
     where you get the password values from the system admins or Jim.
     (The db.password and cdw.password can be the same.)
     Do
        chmod 600 .hg.conf
     to make it private
 9) Create a cdw user for the mariaSql database and also a cdw database that
    the cdw user has full authorities for.
 10) Copy over the validation data from hgwdev
        cd /data/cirm
        scp -rp hgwdev:/data/cirm/valData .
 11) Create the table structure for the cdw database by logging into mysql,
     doing
        hgsqladmin create cdw
        hgsql cdw < ~/kent/src/hg/cirm/cdw/lib/cdw.sql;
 12) Populate the settings table by doing
        insert into cdwSettings set name='prefix',val='SSPG';
        insert into cdwSettings set name='schema',val='/data/cirm/valData/tags.schema';
     Note these lines control the prefix to the accession numbers for the files,
     and the tagStorm schema respectively.
-13) Set up users for cdw system, people who can submit files:
-        cdwCreateUser kent@soe.ucsc.edu
-        hgsql -e "update cdwUser set isAdmin=1 where email='kent@soe.ucsc.edu'" cdw
-	cdwCreateUser mhaeussl@ucsc.edu
-	cdwCreateUser wisulliv@ucsc.edu
-14) Run script to load up validations:
-        ~/kent/src/hg/cirm/cdw/initQa
+13) Set up users and groups for cdw system, people who can submit files and groups they
+    belong to.  You'll need to edit this script for different installations.
+       ~/kent/src/hg/cirm/cdw/install/initUsersGroups
+14) Run script to load up validation and quality assurance files
+        ~/kent/src/hg/cirm/cdw/install/initQa
 15) Find the following bioinformatics programs and make them accessible to the cdw user.
 	 tabix (version 0.2.5 is what we use)
 	 bgzip (part of Heng Li's tabix kit)
 	 bowtie (we use version 1.3.1)
 16) Set up the bowtie indexes in ramdisk.  (redo on reboot)
 	rsync -apv /data/cirm/valData/ramdisk/ /dev/shm/btData/
 17) Start up the daemons (redo on reboot)
 	cd /data/cirm/cdw
 	cdwRunDaemon cdw cdwJob 30 -log=cdwQa.log
     Sometimes the daemons will crash out.  Usually it's on a new data type. Do a
         ps -u cdw
     to see if this has happened.  If so then do
         killall cdwRunDaemon
     have a look at the cdwJob.log,  and possibly the latest entries in the cdwJob
     database table, and then do cdwRunDaemon again as above to restart.