45d3e9c5ce59d3034e38de40df155c1cf89121a1
kent
  Tue Oct 1 14:24:41 2024 -0700
Adding a few more things to install instructions for cdw.

diff --git src/hg/cirm/cdw/install/README src/hg/cirm/cdw/install/README
index cf4c9cd..7dbe93e 100644
--- src/hg/cirm/cdw/install/README
+++ src/hg/cirm/cdw/install/README
@@ -1,42 +1,51 @@
 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
-	/data/cirm
+	$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.
@@ -47,25 +56,29 @@
     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
-15) Start up the daemons
+15) Find the following programs and make them accessible to the cdw user.
+         bowtie 
+	 tabix (version 0.2.5 is what we use)
+	 bgzip (part of Heng Li's tabix kit)
+16) Start up the daemons
 	cd /data/cirm/cdw
 	cdwRunDaemon cdw cdwJob 5 -log=cdwJob.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.