Merge pull request #26 from wtsi-npg/devel

pull changes from wtsi devel to my devel
switch to samplesheet driver if NPG_CACHED_SAMPLESHEET_FILE is set; samplesheet driver - ensure that spiked_phix_tag_index is defined for a pool
pulled changes from wtsi-devel
Changes and new conf files to run teh tracking server under apache2.2
reverted accidentally changed shebang line of one of CGI scripts; Changes and MANIFEST updated; hardcoded link to enigmatic authentication page
added missing definition of dev for cgi-bin location
secure PATH definition is needed to read staging areas free space
local PATH definition for the CGI script; global definition seems to interfere with mod perl
links to staging area server are picked up from config ...

"staging_url" parameter, and so are relative (to current host and port) if this is empty or non-existent
Merge pull request #113 from wtsi-npg/devel

Fix tests skipped; use scratch109
Merge pull request #27 from dkj/apache_sfweb

links to staging area server are picked up from config ...
Changes: remove typos&update
remove outdated apache config file
correct listing of files in MANIFEST
specify customised location for APACHE_LOCK_DIR
apache configuration files changed to ensure that, for mod_perl, @INC is extended at server start up; use /cgi-bin/ url for enigmatic instead of /perl/ to restrict mod_perl apps on the prod webteam server to tracking and npgqc only
apache configuration: infer NPG_TRACKING_SERVER_PATH from $APACHE_CONFDIR since we set this variable explicitly; set dev to "live" explicitly rather than not setting it, otherwise will have to use -D flags as apache args
update modification time of the daemon pid file when pinging to avoid deletion of this file from /tmp on Ubuntu precise
correct release numbers
Merge pull request #114 from mgcam/pingable_daemons

ensure ability to ping and stop daemons is not lost over time