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