Using a Computer

I’ve been working on installing the stripped-down open source genome browser, GBrowse, onto my computer. In order to do all this cool sequencing stuff I’m planning, I’ve got a lot of computer-learning curve to overcome. One thing that will be extremely useful both for learning and for our future plans will be to build my own Haemophilus influenzae genome browser.

So GBrowse installation looks pretty easy. But I do need to have various things installed (and configured properly) for it to work:

• Apache (a webserver),
• PHP (a webpage-writing scripting language),
• MySQL (a database language),
• Perl (a scripting language that’s useful for manipulating text),
• Bio-Perl (a set of modular programs written in Perl),
• and finally of course, GBrowse.

After that, I can add in my genome data in the form of GFF3 files and take it from there. (A BioPerl module will convert normal GenBank files into GFF3 files that the browser wants.) In the future, I hope to align the sequenced isolates into the browser, have some annotations, and eventually add custom tracks representing my sequencing runs.

Luckily all of these packages are open-source and freely available on the web. Unluckily, my skills on the UNIX command line are slow, and my ability to understand system files are apparently extremely limited.

I initially caused all sorts of havoc to my computer trying to get the basic Apache and PHP set-up working. If functioning properly, I should be able to serve my own webpages and see them in my browser. No such luck. After digging around in some forums, I found that many had similar problems, so started mucking around with sensitive system files as recommended on these forums.

This involved uncommenting out some lines of some seriously ugly looks configuration files used by Apache and making sure that I had permission to view my own webpages... I never made it work the way it was supposed to. I feel comfortable enough with text editors and the basic stuff on the command line, but I really don’t understand the hierarchy of the directories in UNIX. I’m sure that most of my problems are stemming from that.

Fortunately, I had actually been taking notes on everything I was doing to my computer! So I could back out and start over. I also discovered that some clever programmers had made things a lot easier for me by having back-ups of a lot of files around.For example the apache2.conf file that I’d tinkered with could simply be replaced by the apache2.conf.default that was sitting right there in the directory with it, so at the command line: cp apache2.conf.default apache2.conf

Next I discovered an easy way out: XAMPP, which was written specifically for the computer semi-literate to make all the configuring happen smoothly. I installed it, and Presto! Apache, PHP, and MySQL up and running with default localhost webpages appearing in my browser magically. WHEW!

Okay, so moving onto GBrowse... I already have Perl, and GBrowse has a handy install script that will get me BioPerl along with GBrowse itself. This ended up taking forever, because the CPAN mirror (which carries all the Perl stuff) kept kicking me off. Eventually, it all seemed to install, and I got a happy message:

########################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
########################################################

But to NO AVAIL! The web address didn’t work, and I couldn’t find that INSTALL file for the life of me. (There’s a lot of files entitled INSTALL.) Criminy, I could already tell what happened, and more forum-searching, and more tinkering, it doesn’t matter because I still couldn’t fix it... Paths. My programs are looking for each other in the wrong locations.

XAMPP’s MySQL got broken, and Apache didn’t know where to look for GBrowse. I actually haven’t found it myself yet. So no dice. I need to figure out how to redirect the Paths, such that the XAMPP installation knows where GBrowse is sticking itself and XAMPP needs to know what happened to MySQL after installing BioPerl and GBrowse. Since I can’t tell those things myself, I guess I’m going to have to go back to the drawing board again...

Sigh... So close yet so far. But the note-taking has been utterly crucial. I, like Rosie, have always thought that I was doing “preliminary analysis” when using my computer for something other than Microsoft Office or Firefox, so always have to repeat work. But especially mucking around with my system files, I’m truly glad I kept track.

It may almost be time to wrassle up a real computer person to give me a hand...