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Old 03-06-2012, 08:55 AM   #1
pepperoni
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Default Do I have to install velvet twice to run color and base space?

Hello, I want to install velvet to run sometimes sequence space (454), some times color space (SOLiD), and sometimes both.I see that in the installation manual it says:
Quote:
2.2
Compiling instructions
From a GNU environment, simply type:
> make
2.3
2.3.1
Compilation settings
Colorspace Velvet
To produce the colorspace version of Velvet, compile with the instruction:
> make color
All the rest of the manual remains valid, except that the executables are
now called velveth de and velveth de .
Beware that color- and sequence space are incompatible, hence separate sets
of executables. In other words, donít try to hash sequence files with colorspace
velvet or vice-versa, under penalty of meaningless results!
I don't understand what does that mean? if I compile for colorspace then I cannot use base space and vice versa? do I have to install it twice in order to use either format?
thanks
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Old 03-06-2012, 09:46 AM   #2
twaddlac
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Default

Yes - the colorspace and basespace aware flavors are not backwards compatible. You don't have to install them both, you just need to compile both types and use them for their respective jobs. I have compile the executable for both cs and bs in the same directory and they work fine.

I hope that answers your questions!
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Old 03-06-2012, 10:24 AM   #3
pepperoni
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thank you very much,
so I type make and then make color I will get both executables, is that right?
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Old 03-06-2012, 10:29 AM   #4
twaddlac
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Yep. I don't know how Velvet handles the settings for each compilation (i.e. if you set 'maxkmerlength=32' for colorspace, I don't know if that would carry over to basespace or if the latter compilation would overwrite it) so keep that in mind if you experience problems. The safest bet would be to compile them both with the same parameters.
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Old 03-06-2012, 10:32 AM   #5
pepperoni
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thank you very much
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454 assembly, color space, hybrid assembly, velvet

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