Installing perl packages locally

We’ve all been there -someone gives you some prewritten code to run and the first thing you try to do fails

 

[loggedin@host ~]$ ./prepared_script.pl -i infile -o outfile

Can’t locate Package/1.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 at ./prepared_script.pl line 17.

So whats the problem? Well, essentially it is that the perl module (in this case it would be Package::1) isn’t available from your installation

The solution. You need to install the perl module (Package::1) into a local library and point perl at it.  Here’s how…

1. find your package and download to your server

wget http://www.whereever.url/Package_1.tar.gz

2. untar and navigate into the directory

tar -zxvf Package_1.tar.gz

cd Package_1

3. build makefile specifying your local lib location

perl Makefile.PL PREFIX=~/lib/perl5 LIB=~/lib/perl5

make

make test #this will highlight other missing dependencies…

make install

4. point perl to this library – easiest way is to add the following line to your login via  ~/.bashrc in your favourite editor

export PERL5LIB=~/lib/perl5/  # save then  source the file  (source ~/.bashrc)

5. go back and do it all over again until it all works wonderfully

6. discover that the script you were given doesn’t do what you want anyway….

 

Finally got my visa…will do research for food

So, after months of not being able to work here in the UK, I finally have my visa and can find a salary.  A friend once said to me, “academics are never unemployed, only under salaried ” and in many respects this is true.  I haven’t received a research salary (to do evolutionary biology) in a long time, yet I’m busier than ever.  How does that work?  Well, for one thing, I’ve been retraining myself in NGS analysis techniques, learning and working on RADtag analysis and RNAseq.  I did this because it is likely that I will move around a lot in the coming years as my wife and I are both researchers.  Being bound only to a computer and an internet connection makes being productive much easier (and its fun – the bioinformatics, not the moving), Also since moving to the UK when we left Panama, I have been prohibited from working – it says so in my passport – while the border agency evaluates my claim.  To me it was simple – my wife is Finnish, we are married, she has a job in the UK, so I am allowed to work under several european treaties – the whole process is a rubber stamp.  As it turns out, there are literally thousands of people for whom it is “just a rubber stamp” and I had to (figuratively) stand in line just like everyone else.  Unluckily for me, that meant surrendering my passport while a decision was made.  It took many months (forever?), and meant I had to cancel conference attendances and reschedule meetings.  Finally, as summer drew to a close my visa was approved.  It was a rubber stamp exactly as expected, but boy were those lines long…

So now I can find a salary.  Anyone got a job for me?…

So far so good…

Well the new site has been up for a week and like the title says, so far so good.

Not that anyone has visited it yet, unless it was by accident (a quick check of google analytics reveals that nope, its just been me).  Not that surprising really as I haven’t added the site to my email signature or told anyone of its existence because its only half complete.  Embryonic.  The front (landing) page is looking ok, but I think I’ll have to add a banner to it to jazz it up.  I’m kind of liking the simplicity of it for the moment but it definitely needs some pictures at least somewhere.  As for the rest of the site, well I have grand plans, but I’m also incredibly busy at work – always.  A friend sent me a link to some new tunes on NPR music this morning so at least the sound in my office has been new (to me).

Thats all for today though, the beasts are hungry…

Bloggery

Well here is my first blog post-

I will populate these pages with a variety of “interesting” things.  By that, I mean interesting to me…

 

What do I do on a blog? of what shall I blog?  every blog needs a theme doesn’t it, or does it?  Can’t it be just a log of stuff, like that doodle pad that was kept by the phone.  remember when a phone was plugged into a wall and if you wanted to use “the” phone thats where you had to go?  Then along came more than one phone in each house, then mobile phones, then the intenet.  Now my mother (hi mum!) is figuring out howto use Skype from her TV!  seriously “change the channel soI can talk to…”!  what was I talking about?  i’m so old, i remember a life before mobile phones, before the internet, before wifi, before smartphones.  I remember a life less…damn i’m easily distracted.

Back to that doodle pad next to the phone…there was no constant theme to the conversations that took place on the phone, and neither was there a theme to the doodles in the pad.  If you felt the need to write something down you just did.  No thinking about what else was onthe pad, just write what you needed to write.  or draw, or doodle.

Well this blog is going to be a lot like that doodle pad. My blog shall be about whatever takes my fancy at the time.  Sure, most posts will likely be about research things that , but I also have a strong interest in photography, about travelling, what annoys me, fighting with my inner child, . I go to the gym a bit and lift heavy things so I might post about what Im doing there, more as a record for myself of what im doing there and thinking about (I approach most things in my life from a pretty scientific view).  I’ll probably also post things like a few recipes and other bits and pieces  Mostly I go to work and play with very large datasets that I create by measuring very small things, that will be most definitely blogged about.

 

Now, time to figure out what to do with this site…