NOTES.txt

- If mtDNA-server.pl fails check that the optional paramaters div is not deactivated via jquery in js/main.js
- If sqs fails empty files
  data/.sqs/
sqs.queue.debug*
sqs.pid.www-data*

- After Perl upgrade 'endform' in CGI.pm needs to be 'end_form' otherwise you will get bareword error

setfacl -b /media/mrueda in order to have access to user 'www-data'
Make sure that www-data has access to all files spread around (media/mrueda/2TB/genomes)
http://serverfault.com/questions/272551/how-do-you-give-execute-permissions-to-apache2-user-and-not-to-everyone-else

$ groups www-data
www-data : www-data mrueda

user apache has no login shell (/sbin/nologin) in /etc/passwd)
su -s /bin/sh apache -c "whoami"
or change it in /etc/passwd

SElinux in CentOs7 blocks access to directories from user 'apache'
su -s /bin/sh apache -c "whoami"

if json gives trouble try clearing cache Chrome
64  systemctl status httpd.service
  665  journalctl -xe
  666  sudo journalctl -xe
  667  sudo semanage fcontext -a -t httpd_sys_rw_content_t /var/www/mtDNA
  668  sudo restorecon -RF /var/www/mtDNA
  669  sudo apachectl restart
  670  sudo journalctl -xe
  671  setsebool -P httpd_unified 1
  672  sudo  setsebool -P httpd_unified 1
  673  sudo apachectl restart
  674  history

#chomd 700 .ssh/
#chmod 600 authorized_keys

/dev/mapper/centos-root   50G   15G   36G  30% /

1440 jobs ( 25Mb job)

index.pl => could not get executed in CentOs Apache2 -> We kept index.cgi
Note that samtools version in MToolBox.sh is 1.3

In production server 'data' is a symbolink link

- The behaviour of upload_div differs in CentOS with respect Ubuntu.
  - Centos we can dispaly if after submit-btn
  - Ubuntu - we can't. We used display:none i+jQuery trick

# when moved from "/" to /mtdna (reverse proxy) form action="." if not using Mojolicius
# AloowOverride All affects the behaviour of divs in roman (uploading div does not work

The same calculation can get slightly different results (see test/test.{1,2} 

start.scripps.edu -> NOTHING WORKS - CHECK THAT 2TB is RUNNING
                                   - check in sqs.pm that number maxqu = #cores
roman.scripps.edu -> When you restart the machine teh first submission creates this message

"17

    Starting qseek daemon for www-data
    on mrueda-ws1 at Fri Jan 13 16:21:48 PST 2017."

So it's better to use head -1 instead of cat

# IndexIgnore * to disable dir read from http

# smtp.scripps.edu is the smtp server, if not configured right the emails will only work withn TSRI addresses.

# Crontab daily at roman
/etc/cron.daily