Hi all,
I solved my server problems and I'm up and running, but sadly the same problem
persists. I can not use the data_manager tools to fetch a reference genome from
file. If I launch the script from the command line I get:
No handlers could be found for logger "galaxy.util.json"
Traceback (most recent call last): File
"/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py",
line 350, in <module> if __name__ == "__main__": main() File
"/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py",
line 335, in main target_directory = params[ 'output_data'
][0]['extra_files_path']KeyError: 'output_data'
So on one hand I get the "no logger" message (same as in the interface) and on
the other hand, looking at the file that is generated by the data_manager I get
a JSON dict without the params_dict or the output_data keys.dataset_XXXXX.dat
consistently gets this kind of content:{"data_tables": {"all_fasta": [{"path":
"sm52.fa", "dbkey": "sm52", "name": "Schistosoma mansoni v5.2", "value":
"sm52"}]}}
Are these two different problems? Could you point me to a solution?
Cheers!CristianFrom: tuto...@hotmail.com
To: dannon.ba...@gmail.com
Date: Thu, 4 Dec 2014 16:01:53 +0000
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] No handlers could be found for logger
"galaxy.util.json"
Hi Dannon,
I got it running! The problem was the main handler had crashed and (had not
seen that the main.pid was missing).I restarted the server and everything is
running now.
Sorry for the waste of time!Cristian
From: tuto...@hotmail.com
To: dannon.ba...@gmail.com
Date: Thu, 4 Dec 2014 15:47:00 +0000
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] No handlers could be found for logger
"galaxy.util.json"
Hi Dannon,
I started the installation of the server about a month or so back. I did a hg
update -U recently...
$ hg tipchangeset: 14854:26aab19109cebranch: stabletag: tipuser:
Nate Coraor <n...@bx.psu.edu>date: Thu Nov 27 09:00:14 2014
-0500summary: Update tag latest_2014.10.06 for changeset acb2548443ae
Any ideas?Cristian
Date: Thu, 4 Dec 2014 10:22:22 -0500
Subject: Re: [galaxy-dev] No handlers could be found for logger
"galaxy.util.json"
From: dannon.ba...@gmail.com
To: tuto...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org
Hi Cristian,
What revision of Galaxy are you running? I believe this was fixed a while back.
-Dannon
On Thu, Dec 4, 2014 at 10:14 AM, C. Ch. <tuto...@hotmail.com> wrote:
Hi All,
While trying to use the data_manager_fetch_genome_all_fasta to create a
reference genome I get the following error: No handlers could be found for
logger "galaxy.util.json"
I'm on the latest version of galaxy.
Any idea what is wrong?
Thanks!Cristian
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