8cc9219d0990c270849cba2159a27ad9a95a1f08
kent
  Tue Oct 1 17:29:17 2024 -0700
Adding bits about installing bowtie and indexes.  Upping validation threads.

diff --git src/hg/cirm/cdw/install/README src/hg/cirm/cdw/install/README
index 7dbe93e..5fbcadf 100644
--- src/hg/cirm/cdw/install/README
+++ src/hg/cirm/cdw/install/README
@@ -56,29 +56,31 @@
     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) Find the following programs and make them accessible to the cdw user.
-         bowtie 
+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)
-16) Start up the daemons
+	 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 5 -log=cdwJob.log
+	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.