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
University of Alabama at Birmingham