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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