Hi Curtis,

Sorry for the trouble in using the converter package. I will fix the issues
which you mentioned below.

For a quick fix, I can point you to my working repository:
https://github.com/vipints/GFFtools-GX

This program will help you to convert the gff to 12 column bed file:
https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.py

the associated galaxy wrapper:
https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.xml

I know this is not the best way to fix the issue but I will update the
public repository soon.

Vipin | Rätsch Lab

On Mon, Apr 6, 2015 at 4:35 PM, Curtis Hendrickson (Campus) <curt...@uab.edu
> wrote:

>  Folks
>
>
>
> I installed this very useful looking tool repository (fml_gff3togtf
> <https://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf>)  to convert
> GFF3->BED12 based on this BioStars.
>
>                 https://www.biostars.org/p/85869
>
> It installed fine, but when I run it on
>
>
> ftp://ftp.ncbi.nih.gov/genomes/Viruses/Human_herpesvirus_5_uid14559/NC_006273.gff
>
> I get
>
> Traceback (most recent call last):
>
>   File "/share/apps/galaxy/test-shed-tools/
> toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/gff_to_bed.py",
> line 18, in <module>
>
>     import GFFParser
>
>   File "/share/apps/galaxy/test-shed-tools/
> toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/GFFParser.py",
> line 20, in <module>
>
>     import scipy.io as sio
>
> ImportError: No module named scipy.io
>
> Anyone know the trick to get the python libraries set up correctly?
>
>
>
> (also note that this failed nightly tests on 2015-04-06 – but that looks
> like a lack of test data/configuration)
>
>
>
> I see some other packages (like htseq_count
> <https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count>) have numpy as
> a dependency…. Using the devteam’s numpy 1.7 package:
>
>
> https://toolshed.g2.bx.psu.edu/view/devteam/package_numpy_1_7
>
>
>
> Regards,
>
> Curtis
>
>
>
> Research Associate, Informatics Unit
>
> Center for Clinical and Translational Science
>
> http://bioinformatics.uab.edu
>
> University of Alabama at Birmingham
>
>
>
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