Installed tools not working on galaxy 16.07

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1

Hi,
I’ve inherited a legacy galaxy (version 16.07) installed on local Ubuntu (18.04) server, with a lot of installed tools. However, when I try to do data analysis I get the error ‘Fatal error: Exit code 1 ()’. Here is the bug report for simple fastqc (Note: I got the same/similar error message for other tools I’ve tried too).
Fatal error: Exit code 1 ()
/bin/sh: 1: fastqc: not found
Traceback (most recent call last):
File “/home/posavi/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3a458e268066/fastqc/rgFastQC.py”, line 166, in
fastqc_runner.run_fastqc()
File “/home/posavi/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3a458e268066/fastqc/rgFastQC.py”, line 139, in run_fastqc
subprocess.check_call(self.command_line, shell=True)
File “/usr/lib/python2.7/subprocess.py”, line 190, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘fastqc --outdir /home/posavi/galaxy/database/jobs_directory/017/17999/dataset_35883_files --quiet --extract -f fastq tenM.fastq’ returned non-zero exit status 127
Also, most of the installed tools have either red arrow or red triangle flag (see the image)

image
image2640×1530 451 KB

I am also not able to either update/reinstall any of installed tools neither to install any new tools.
Please let me know if there is the way to fix this problem, except to upgrade ubuntu and galaxy.
Thank you.
Marijan

2

Hi @Marijan

This is a configuration problem. Was the Galaxy installation moved to a new location?

You’ll need to be running a current version of Galaxy for the newer tool versions to be functional.

Upgrading works best when done sequentially through releases. For your case, that would be a lot of work. Is there a reason why you need the older installation instead of starting over?

3

Hi Jennifer,

Thank you very much for your prompt response.

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