Folks

 

I installed this very useful looking tool repository (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) 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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