Question: FastQ Groomer Problem - Syntax
0
gravatar for tony.shu
12 months ago by
tony.shu10
tony.shu10 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 • 334 views
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 12 months ago by tony.shu10
0
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson25k
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