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Old 11-03-2009, 07:06 AM   #1
zcsbldm
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Default How to install GAPapiline on MAC

Hello, everyone.

I'm from China, and my teacher told me to use ELAND to do analysis as a practise, She said the GAPipeline contains the ELAND. now I just use MAC operate system for several weeks.

Are there any instrcution files for me to install it on MAC? I download "GAPipeline-1.1rc1"

I read the "GAPipeline installatoin.html", and it says I need a lot other softwares such as gnuplot, FFTW... but I found these three files "ELAND_standalone.pl","ELAND_test","CMakeLists.txt" at "/Pipeline/perl/alignment"

If I just want to use ELAND, I don't know whether it necessary to install other softwares. Maybe I am just not familiar with MAC...

Best thank for you!
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Old 11-03-2009, 11:26 AM   #2
dawe
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Quote:
Originally Posted by zcsbldm View Post
If I just want to use ELAND, I don't know whether it necessary to install other softwares. Maybe I am just not familiar with MAC...
The build chain for GA Pipeline is a developer nightmare. Illumina people made some step ahead starting with GA 1.3, as they introduced cmake projects.
If you are able to read a makefile and bypass dependencies you should be able to build eland alone. Nevertheless it would be better to install all the pipeline software (also because eland alone is almost useless, today).
If you are running OS X you can install all the dependecies with MacPorts (just read the howto pages).
Consider that Illumina software is full of bugs and if you are running on PPC architecture you may experience some segfaults (actually I only guessing...).
Consider also that current version of pipeline is 1.4 (I've seen manuals for 1.5) which has a different quality scoring code for reads.
I would spend my two cents on any other aligner discussed in this form, not only eland.

HTH

d
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Old 11-03-2009, 04:16 PM   #3
seq_GA
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Hi dawe,

Are you using any other tool instead of eland?
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Old 11-03-2009, 06:44 PM   #4
drio
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It should be that complicate. All the thirty parties illumina uses are pretty open source standard. Try to compile the denpendicnes yoursef (fftw/gnuplot) or as suggested, use macports.

If the only thing you want to do is to finish the GERALD step from the RTA just install some virtualization software and install Linux. It will be a little bit slower but current virtualization tools are crazy fast. And of course the installation of GApipeline is trivial.

Let us know how it goes.

-drd
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Old 11-03-2009, 06:46 PM   #5
drio
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Quote:
Originally Posted by seq_GA View Post
Hi dawe,

Are you using any other tool instead of eland?
And yes.. use eland if you want to get the basic run stats but realign
_all_ the data with another aligner... please.

I'd suggest bfast, maq or bwa. It depends what you want to do.
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