[Bio-Linux] Bio-Linux Digest, Vol 82, Issue 3 PROBLEM SOLVED --

Fri Jul 17 14:22:42 EDT 2015

Hi, 

So now I reinstalled  BioLinux 8 with the same .iso file (using a usb stick though)

I only left the ‘Download updates while installing’ unchecked this time. Now Galaxy works!

Maybe it had something to do with the updates that had been installed during the first installation of biolinux. My best guess.

Anyway,  it works now, which is great.  Really appreciate the preinstalled bioinfo packages.

Thank you very much for your support. 

Best, Julian.

From: "Julian Jäger" [mailto:jaeger.julian at gmx.net] 
Sent: 16 July 2015 22:50
To: Julian Jaeger
Subject: Re: Re: Bio-Linux Digest, Vol 82, Issue 3

@tony: I checked the installation dvd, no errors found. 

Thanks for any help so far. I could try a newinstallation, but not sure if this will fix it. 

Any more ideas? Thanks, Julian
-- 
Sent from my Android phone with GMX Mail. Please excuse my brevity.

Julian Jaeger <juls.jaeger <http://juls.jaeger> @gmx.de> wrote:

Thanks for the replies.

@TIM: here (see below) is the output of sudo -u Debian-galaxy ls
-l /usr/lib/galaxy-server --color=auto
:(nothing red, only green and blue-ish ones.

@Tony: I did a clean installation on the new build desktop PC using
the .iso (burn on dvd).

This is by the way the message when I want to start galaxy:

"The Galaxy server doesn't seem to be running on your machine.
You may need to start it with the command:

sudo start galaxy

Or else Galaxy may still be starting up (it takes a couple
of minutes to get going on the first run)."

output from sudo -u Debian-galaxy ls -l /usr/lib/galaxy-server
--color=auto

I will check the media dvd now.

total 168
-rw-r--r-- 1 root root 6862 Aug 12 2014 bl_data_manager_conf.xml
-rw-r--r-- 1 root root 3570 Aug 19 2014 bl_tool_conf.xml
drwxr-xr-x 14 root root 4096 Dec 10 2014 bl_tools
-rwxr-xr-x 1 root root 4101 Aug 19 2014 buildbot_setup.sh
-rwxr-xr-x 1 root root 60 Aug 19 2014 create_db.sh
drwxr-xr-x 2 root root 4096 Jul 14 07:53 cron
lrwxrwxrwx 1 root root 31 Jul 14 07:44 database
-> /var/lib/galaxy-server/database
lrwxrwxrwx 1 root root 40 Jul 14 07:44 data_manager_conf.xml
-> /etc/galaxy-server/data_manager_conf.xml
lrwxrwxrwx 1 root root 37 Jul 14 07:44 datatypes_conf.xml
-> /etc/galaxy-server/datatypes_conf.xml
drwxr-xr-x 8 root root 4096 Jul 4 2014 display_applications
-rw-r--r-- 1 root root 2703 Aug 19 2014 dist-eggs.ini
drwxr-xr-x 31 root root 4096 Dec 10 2014 eggs
-rw-r--r-- 1 root root 2202 Aug 19 2014 eggs.ini
drwxr-xr-x 2 root root 4096 Dec 10 2014 external_service_types
lrwxrwxrwx 1 root root 50 Jul 14 07:44
external_service_types_conf.xml
-> /etc/galaxy-server/external_service_types_conf.xml
-rwxr-xr-x 1 root root 146 Aug 19 2014 extract_dataset_parts.sh
-rwxr-xr-x 1 root root 2023 Dec 3 2013 goto_galaxy.sh
lrwxrwxrwx 1 root root 57 Jul 14 07:44 integrated_tool_panel.xml
-> /var/lib/galaxy-server/database/integrated_tool_panel.xml
drwxr-xr-x 5 root root 4096 Jul 14 07:53 lib
drwxr-xr-x 5 root root 4096 Dec 10 2014 locale
-rwxr-xr-x 1 root root 1430 May 14 2014 make_transfer_dirs.sh
-rwxr-xr-x 1 root root 238 Aug 19 2014 manage_db.sh
-rwxr-xr-x 1 root root 63 Aug 19 2014 manage_tools.sh
lrwxrwxrwx 1 root root 42 Jul 14 07:44 migrated_tools_conf.xml
-> /etc/galaxy-server/migrated_tools_conf.xml
-rwxr-xr-x 1 root root 160 Aug 19 2014 run_demo_sequencer.sh
-rwxr-xr-x 1 root root 5959 Aug 19 2014 run_functional_tests.sh
-rwxr-xr-x 1 root root 153 Aug 19 2014 run_galaxy_listener.sh
-rwxr-xr-x 1 root root 914 Aug 19 2014 run_reports.sh
-rwxr-xr-x 1 root root 1835 Aug 18 2014 run.sh
-rwxr-xr-x 1 root root 849 Aug 19 2014
run_tool_shed_functional_tests.sh
-rwxr-xr-x 1 root root 442 Aug 19 2014 run_tool_shed.sh
-rwxr-xr-x 1 root root 754 Aug 19 2014 run_unit_tests.sh
drwxr-xr-x 15 root root 4096 Jul 14 07:53 scripts
-rwxr-xr-x 1 root root 63 Aug 19 2014 set_metadata.sh
-rwxr-xr-x 1 root root 101 Aug 19 2014 setup_rabbitmq.sh
lrwxrwxrwx 1 root root 60 Jul 14 07:44 shed_data_manager_conf.xml
-> /var/lib/galaxy-server/shed_tools/shed_data_manager_conf.xml
-rw-r--r-- 1 root root 55 Aug 19 2014
shed_data_manager_conf.xml.sample
lrwxrwxrwx 1 root root 52 Jul 14 07:44 shed_tool_conf.xml
-> /var/lib/galaxy-server/shed_tools/shed_tool_conf.xml
-rw-r--r-- 1 root root 66 Aug 19 2014 shed_tool_conf.xml.sample
lrwxrwxrwx 1 root root 63 Jul 14 07:44 shed_tool_data_table_conf.xml
-> /var/lib/galaxy-server/shed_tools/shed_tool_data_table_conf.xml
-rw-r--r-- 1 root root 41 Aug 19 2014
shed_tool_data_table_conf.xml.sample
lrwxrwxrwx 1 root root 33 Jul 14 07:44 shed_tools
-> /var/lib/galaxy-server/shed_tools
lrwxrwxrwx 1 root root 32 Jul 14 07:44 static
-> ../../share/galaxy-server/static
lrwxrwxrwx 1 root root 35 Jul 14 07:44 templates
-> ../../share/galaxy-server/templates
lrwxrwxrwx 1 root root 30 Jul 14 07:44 test
-> ../../share/galaxy-server/test
lrwxrwxrwx 1 root root 35 Jul 14 07:44 test-data
-> ../../share/galaxy-server/test-data
lrwxrwxrwx 1 root root 32 Jul 14 07:44 tool_conf.xml
-> /etc/galaxy-server/tool_conf.xml
-rw-r--r-- 1 root root 6357 Aug 19 2014 tool_conf.xml.main
lrwxrwxrwx 1 root root 32 Jul 14 07:44 tool-data
-> /var/lib/galaxy-server/tool-data
lrwxrwxrwx 1 root root 43 Jul 14 07:44 tool_data_table_conf.xml
-> /etc/galaxy-server/tool_data_table_conf.xml
-rw-r--r-- 1 root root 2612 Aug 19 2014 tool_list.py
-rw-r--r-- 1 root root 2167 Jul 14 07:53 tool_list.pyc
drwxr-xr-x 20 root root 4096 Dec 10 2014 tools
lrwxrwxrwx 1 root root 38 Jul 14 07:44 tool_sheds_conf.xml
-> /etc/galaxy-server/tool_sheds_conf.xml
lrwxrwxrwx 1 root root 34 Jul 14 07:44 universe_wsgi.d
-> /etc/galaxy-server/universe_wsgi.d

On Thu, 2015-07-16 at 12:00 +0100,
bio-linux-request at nebclists.nerc.ac.uk <mailto:bio-linux-request at nebclists.nerc.ac.uk>  wrote:
> Send Bio-Linux mailing list submissions to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
> 1. Re: FW: Galaxy on Bio-Linux 8 does not start. 'ExpatError'
> (Tim Booth)
> 2. has anyone compiled Bio-linux to run on raspberry Pi 2
> (Duleep Samuel)
> 3. Re: has anyone compiled Bio-linux to run on raspberry Pi 2
> (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Jul 2015 12:15:56 +0100
> From: Tim Booth <tbooth at ceh.ac.uk <mailto:tbooth at ceh.ac.uk> >
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk <mailto:bio-linux at nebclists.nerc.ac.uk> >
> Subject: Re: [Bio-Linux] FW: Galaxy on Bio-Linux 8 does not start.
> 'ExpatError'
> Message-ID:
> <1436958956.5659.129.camel at wllt1771.nerc-wallingford.ac.uk <mailto:1436958956.5659.129.camel at wllt1771.nerc-wallingford.ac.uk> >
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Julian,
>
> I've not seen this error before. It looks like it is trying to load
> one
> of the tool configuration files and the file is either missing or
> empty,
> so it seems there is a problem with the installation.
>
> Galaxy should run automatically and I've tested this on a fresh
> Bio-Linux 8 installation. To manually control it you can run "sudo
> stop
> galaxy" or "sudo start galaxy" but other ways of running the server
> might not work.
>
> To see if files are missing please run:
>
> sudo -u Debian-galaxy ls -l /usr/lib/galaxy-server --color=auto
>
> Does anything show up in red? Can you please post the listing you
> get?
>
> Cheers,
>
> TIM
>

Message: 2
Date: Wed, 15 Jul 2015 10:26:29 +0100
From: Tony Travis <tony.travis at abdn.ac.uk <mailto:tony.travis at abdn.ac.uk> >
To: <bio-linux at nebclists.nerc.ac.uk <mailto:bio-linux at nebclists.nerc.ac.uk> >
Subject: Re: [Bio-Linux] Galaxy on Bio-Linux 8 does not start.
'ExpatError'
Message-ID: <55A62745.8020706 at abdn.ac.uk <mailto:55A62745.8020706 at abdn.ac.uk> >
Content-Type: text/plain; charset="windows-1252"

On 15/07/15 10:09, Julian Jaeger wrote:
> Hi everyone!
>
> I just installed Bio-Linux 8, which has Galaxy on board. Unfortunatly
> Galaxy won't start.
>
> Here is the recent traceback from the logfile:
> [...]

Hi, Julian.

How did you install Bio-Linux 8?

Galaxy is working fine for me either from the 'live' USB-stick or when
installed onto the hard disk. You might have problems if you upgraded an
existing system. Another thing to check is that your installation media
is free from errors (run check the media from the boot menu).

Bye,

Tony.

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