Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: FastQ Groomer Problem - Syntax
0
gravatar for tony.shu
17 months ago by
tony.shu • 10
tony.shu • 10 wrote:

Hi,

I have searched all over and I cannot find a solution to this. When I run the FastQ groomer I have installed through the tool shed, I get this in the history:

File "/project/sysbio/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/e4d28c94242d/fastq_groomer/fastq_groomer.py", line 29

print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )
                                         ^

SyntaxError: invalid syntax

I have python 2.7.8 and run galaxy locally. I have not included a: from __future__ import print_function anywhere. When running the FastQ Groomer tool, my inputs are:

fname.fastq

Sanger & Illumina 1.8+

basic

Any help will be appreciated, thanks.

Tony
fastq software error devteam • 482 views
ADD COMMENT • link •
modified 17 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by tony.shu • 10
0
gravatar for Jennifer Hillman Jackson
17 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This appears to be a tool install problem. Make sure that you are using the latest version of Galaxy (17_05) and the most recent version of FastQC. Use the default conda dependency resolution for best results, unless you are configuring a specific system as an administrator and can troubleshoot locally.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 174 users visited in the last hour