Question: Pacific Biosciences pitchfork installation
0
gravatar for Roxane Boyer
3 months ago by
Roxane Boyer180
France/Marseille/IBDM
Roxane Boyer180 wrote:

Hi everyone !

I'm currently working on a genome assembly with Pacific Biosciences long reads, and to finish my assembly, I need to polish it using quiver. My problem is that, whether using their tool box called pitchfork, where quiver is installed automatically, or installing it manually with all the required PacBio dependencies, I fail to install it.

My main problem is that I don't understand clearly the instructions for pitchfork installation : - PacBio pitchfork link : https://github.com/PacificBiosciences/pitchfork - PacBio pitchfork installation guide : https://github.com/PacificBiosciences/pitchfork/wiki

The first lines of the pitchfork installation guide are the followings :

git clone git://github.com/PacificBiosciences/pitchfork
cd pitchfork
make PREFIX=/tmp/pitchfork blasr

It says that, if PREFIX is not specified, then a directory will be automatically choose at "pitchfork/deployment/". But I can't figure out what this PREFIX is for. So I tried this lines anyway and it worked :

git clone git://github.com/PacificBiosciences/pitchfork
cd pitchfork
make blasr

But then, to run quiver, you have also ton run pbalign before, so I tried make with the target "pbalign", and then I got an error :

Copying the static library to /home/loutre/pitchfork/staging/OpenBLAS-0.2.18/lib
Copying the shared library to /home/loutre/pitchfork/staging/OpenBLAS-0.2.18/lib
install: impossible d'évaluer «libopenblas_sandybridgep-r0.2.18.so»: Aucun fichier ou dossier de ce type

It says that it couldn't find the libopenblas library, I think that all my problem are a matter of path, and that I may miss something with this "settings.mk" file they show in their tutorial. But as I can't figure out what each variable represent, I couldn't make one myself.

I've asked many questions at Pacific Biosciences themselves on github, but each time they remains very unclear for me.

As it seems that I'm the only one that encounter a problem with pitchfork installation, I'm requiring some help to finally install it by myself.

Does anyone has a an idea of what is going on ? Thanks for your help !

Cheers, Roxane

pacbio quiver software error • 202 views
ADD COMMENTlink written 3 months ago by Roxane Boyer180
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