If you are installing scipy from source (and I think that is how galaxy and pip both do it), then you need a fortran compiler installed. -Will On Mon, Apr 6, 2015 at 1:35 PM, Curtis Hendrickson (Campus) <curtish@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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.