Hi Christopher,
thanks for your quick response.
Yes, there some reasons to install genome browser "the hard way" ..
- we are not running a common flavor of linux, instead we are ruuning our own, home made linux since almost two decades :-)
- we have our own package management system, not rpm, not deb
- I have no root access to any of our servers, so I need to install genome browser in custom "project" with user privileges
- our sysadmins won't install genome browser systemwide, again, I need to install it somewhere I want to
We have already a few instances running (version from 2012!), the guy who compiled and installed these instances has left the institute and his documentation is poor. I need to setup one or more genome browser instances with our (custom) genomes, I don't need the public data(bases), no hg19 or mm10.
After googling and reading quite a while, I decided to start this way:
- compiling and installing apache httpd
- compiling and installing mysql
- setting some environment variables, MACHTYPE, BINDIR, CGI_BIN, SCRIPTS, DOCUMENTROOT among others
- compiling and installing samtabix, setting USE_SAMTABIX, SAMTABIXDIR
- deflating archive, cd kent/src,
make all
works fine, except the error I reported.
The difficulties I encounter are:
* there is more than one place with similar, but not identical information about the manual installation process, mostly incomplete
* I do not find any resource describing completely the process of compiling and installing genome browser as a mirror without public data, but with custom genomes.
Compiling bins/cgi-bins is one thing, the other things are apache setup (ok, there are some infos, should be manageable), and mysql setup. How is the database setup when I don't want to use/import public data?
All these infos can be deduced from our ancient installation in combination with heavy googling and personal know-how .. that's the hard way :-)
I wish, you'd point me to some resources I have overseen in my attempts to find the "best" way to install genome browser ...
Let me shortly summarize what I try to accomplish:
* genome browser installation from source, mirror
* no public data, exclusively custom genomes and annotations
* custom linux system (64bit), no root access and no possibilty to install genome browser systemwide by our IT dep
Updating genome browser is hopefully done by recompiling kent source base ...
best,
Sven