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: tuto345@hotmail.com To: dannon.baker@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 <nate@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.baker@gmail.com To: tuto345@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. <tuto345@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 ___________________________________________________________ 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/ ___________________________________________________________ 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/

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: tuto345@hotmail.com To: dannon.baker@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: tuto345@hotmail.com To: dannon.baker@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 <nate@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.baker@gmail.com To: tuto345@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. <tuto345@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 ___________________________________________________________ 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/ ___________________________________________________________ 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/ ___________________________________________________________ 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/