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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Hi, <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>So now I reinstalled BioLinux 8 with the same .iso file (using a usb stick though)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>I only left the ‘Download updates while installing’ unchecked this time. Now Galaxy works!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Maybe it had something to do with the updates that had been installed during the first installation of biolinux. My best guess.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Anyway, it works now, which is great. Really appreciate the preinstalled bioinfo packages.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Thank you very much for your support. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Best, Julian.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> "Julian Jäger" [mailto:jaeger.julian@gmx.net] <br><b>Sent:</b> 16 July 2015 22:50<br><b>To:</b> Julian Jaeger<br><b>Subject:</b> Re: Re: Bio-Linux Digest, Vol 82, Issue 3<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>@tony: I checked the installation dvd, no errors found. <br><br>Thanks for any help so far. I could try a newinstallation, but not sure if this will fix it. <br><br>Any more ideas? Thanks, Julian<br>-- <br>Sent from my Android phone with GMX Mail. Please excuse my brevity.<o:p></o:p></p><div><p class=MsoNormal>Julian Jaeger <<a href="http://juls.jaeger">juls.jaeger</a>@gmx.de> wrote:<o:p></o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><p class=MsoNormal style='margin-bottom:12.0pt'>Thanks for the replies.<br><br>@TIM: here (see below) is the output of sudo -u Debian-galaxy ls<br>-l /usr/lib/galaxy-server --color=auto<br>:(nothing red, only green and blue-ish ones.<br><br>@Tony: I did a clean installation on the new build desktop PC using<br>the .iso (burn on dvd).<br><br>This is by the way the message when I want to start galaxy:<br><br>"The Galaxy server doesn't seem to be running on your machine.<br>You may need to start it with the command:<br><br>sudo start galaxy<br><br>Or else Galaxy may still be starting up (it takes a couple<br>of minutes to get going on the first run)."<br><br>output from sudo -u Debian-galaxy ls -l /usr/lib/galaxy-server<br>--color=auto<br><br>I will check the media dvd now.<br><br><br><br>total 168<br>-rw-r--r-- 1 root root 6862 Aug 12 2014 bl_data_manager_conf.xml<br>-rw-r--r-- 1 root root 3570 Aug 19 2014 bl_tool_conf.xml<br>drwxr-xr-x 14 root root 4096 Dec 10 2014 bl_tools<br>-rwxr-xr-x 1 root root 4101 Aug 19 2014 buildbot_setup.sh<br>-rwxr-xr-x 1 root root 60 Aug 19 2014 create_db.sh<br>drwxr-xr-x 2 root root 4096 Jul 14 07:53 cron<br>lrwxrwxrwx 1 root root 31 Jul 14 07:44 database<br>-> /var/lib/galaxy-server/database<br>lrwxrwxrwx 1 root root 40 Jul 14 07:44 data_manager_conf.xml<br>-> /etc/galaxy-server/data_manager_conf.xml<br>lrwxrwxrwx 1 root root 37 Jul 14 07:44 datatypes_conf.xml<br>-> /etc/galaxy-server/datatypes_conf.xml<br>drwxr-xr-x 8 root root 4096 Jul 4 2014 display_applications<br>-rw-r--r-- 1 root root 2703 Aug 19 2014 dist-eggs.ini<br>drwxr-xr-x 31 root root 4096 Dec 10 2014 eggs<br>-rw-r--r-- 1 root root 2202 Aug 19 2014 eggs.ini<br>drwxr-xr-x 2 root root 4096 Dec 10 2014 external_service_types<br>lrwxrwxrwx 1 root root 50 Jul 14 07:44<br>external_service_types_conf.xml<br>-> /etc/galaxy-server/external_service_types_conf.xml<br>-rwxr-xr-x 1 root root 146 Aug 19 2014 extract_dataset_parts.sh<br>-rwxr-xr-x 1 root root 2023 Dec 3 2013 goto_galaxy.sh<br>lrwxrwxrwx 1 root root 57 Jul 14 07:44 integrated_tool_panel.xml<br>-> /var/lib/galaxy-server/database/integrated_tool_panel.xml<br>drwxr-xr-x 5 root root 4096 Jul 14 07:53 lib<br>drwxr-xr-x 5 root root 4096 Dec 10 2014 locale<br>-rwxr-xr-x 1 root root 1430 May 14 2014 make_transfer_dirs.sh<br>-rwxr-xr-x 1 root root 238 Aug 19 2014 manage_db.sh<br>-rwxr-xr-x 1 root root 63 Aug 19 2014 manage_tools.sh<br>lrwxrwxrwx 1 root root 42 Jul 14 07:44 migrated_tools_conf.xml<br>-> /etc/galaxy-server/migrated_tools_conf.xml<br>-rwxr-xr-x 1 root root 160 Aug 19 2014 run_demo_sequencer.sh<br>-rwxr-xr-x 1 root root 5959 Aug 19 2014 run_functional_tests.sh<br>-rwxr-xr-x 1 root root 153 Aug 19 2014 run_galaxy_listener.sh<br>-rwxr-xr-x 1 root root 914 Aug 19 2014 run_reports.sh<br>-rwxr-xr-x 1 root root 1835 Aug 18 2014 run.sh<br>-rwxr-xr-x 1 root root 849 Aug 19 2014<br>run_tool_shed_functional_tests.sh<br>-rwxr-xr-x 1 root root 442 Aug 19 2014 run_tool_shed.sh<br>-rwxr-xr-x 1 root root 754 Aug 19 2014 run_unit_tests.sh<br>drwxr-xr-x 15 root root 4096 Jul 14 07:53 scripts<br>-rwxr-xr-x 1 root root 63 Aug 19 2014 set_metadata.sh<br>-rwxr-xr-x 1 root root 101 Aug 19 2014 setup_rabbitmq.sh<br>lrwxrwxrwx 1 root root 60 Jul 14 07:44 shed_data_manager_conf.xml<br>-> /var/lib/galaxy-server/shed_tools/shed_data_manager_conf.xml<br>-rw-r--r-- 1 root root 55 Aug 19 2014<br>shed_data_manager_conf.xml.sample<br>lrwxrwxrwx 1 root root 52 Jul 14 07:44 shed_tool_conf.xml<br>-> /var/lib/galaxy-server/shed_tools/shed_tool_conf.xml<br>-rw-r--r-- 1 root root 66 Aug 19 2014 shed_tool_conf.xml.sample<br>lrwxrwxrwx 1 root root 63 Jul 14 07:44 shed_tool_data_table_conf.xml<br>-> /var/lib/galaxy-server/shed_tools/shed_tool_data_table_conf.xml<br>-rw-r--r-- 1 root root 41 Aug 19 2014<br>shed_tool_data_table_conf.xml.sample<br>lrwxrwxrwx 1 root root 33 Jul 14 07:44 shed_tools<br>-> /var/lib/galaxy-server/shed_tools<br>lrwxrwxrwx 1 root root 32 Jul 14 07:44 static<br>-> ../../share/galaxy-server/static<br>lrwxrwxrwx 1 root root 35 Jul 14 07:44 templates<br>-> ../../share/galaxy-server/templates<br>lrwxrwxrwx 1 root root 30 Jul 14 07:44 test<br>-> ../../share/galaxy-server/test<br>lrwxrwxrwx 1 root root 35 Jul 14 07:44 test-data<br>-> ../../share/galaxy-server/test-data<br>lrwxrwxrwx 1 root root 32 Jul 14 07:44 tool_conf.xml<br>-> /etc/galaxy-server/tool_conf.xml<br>-rw-r--r-- 1 root root 6357 Aug 19 2014 tool_conf.xml.main<br>lrwxrwxrwx 1 root root 32 Jul 14 07:44 tool-data<br>-> /var/lib/galaxy-server/tool-data<br>lrwxrwxrwx 1 root root 43 Jul 14 07:44 tool_data_table_conf.xml<br>-> /etc/galaxy-server/tool_data_table_conf.xml<br>-rw-r--r-- 1 root root 2612 Aug 19 2014 tool_list.py<br>-rw-r--r-- 1 root root 2167 Jul 14 07:53 tool_list.pyc<br>drwxr-xr-x 20 root root 4096 Dec 10 2014 tools<br>lrwxrwxrwx 1 root root 38 Jul 14 07:44 tool_sheds_conf.xml<br>-> /etc/galaxy-server/tool_sheds_conf.xml<br>lrwxrwxrwx 1 root root 34 Jul 14 07:44 universe_wsgi.d<br>-> /etc/galaxy-server/universe_wsgi.d<br><br><br>On Thu, 2015-07-16 at 12:00 +0100,<br><a href="mailto:bio-linux-request@nebclists.nerc.ac.uk">bio-linux-request@nebclists.nerc.ac.uk</a> wrote:<br>> Send Bio-Linux mailing list submissions to<br>> <a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a><br>><br>> To subscribe or unsubscribe via the World Wide Web, visit<br>><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" target="_blank"> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>> or, via email, send a message with subject or body 'help' to<br>> <a href="mailto:bio-linux-request@nebclists.nerc.ac.uk">bio-linux-request@nebclists.nerc.ac.uk</a><br>><br>> You can reach the person managing the list at<br>> <a href="mailto:bio-linux-owner@nebclists.nerc.ac.uk">bio-linux-owner@nebclists.nerc.ac.uk</a><br>><br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of Bio-Linux digest..."<br>><br>><br>> Today's Topics:<br>><br>> 1. Re: FW: Galaxy on Bio-Linux 8 does not start. 'ExpatError'<br>> (Tim Booth)<br>> 2. has anyone compiled Bio-linux to run on raspberry Pi 2<br>> (Duleep Samuel)<br>> 3. Re: has anyone compiled Bio-linux to run on raspberry Pi 2<br>> (Tim Booth)<br>><br>><br>> ----------------------------------------------------------------------<br>><br>> Message: 1<br>> Date: Wed, 15 Jul 2015 12:15:56 +0100<br>> From: Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>> To: Bio-Linux help and discussion <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>> Subject: Re: [Bio-Linux] FW: Galaxy on Bio-Linux 8 does not start.<br>> 'ExpatError'<br>> Message-ID:<br>> <<a href="mailto:1436958956.5659.129.camel@wllt1771.nerc-wallingford.ac.uk">1436958956.5659.129.camel@wllt1771.nerc-wallingford.ac.uk</a>><br>> Content-Type: text/plain; charset="UTF-8"<br>><br>> Hi Julian,<br>><br>> I've not seen this error before. It looks like it is trying to load<br>> one<br>> of the tool configuration files and the file is either missing or<br>> empty,<br>> so it seems there is a problem with the installation.<br>><br>> Galaxy should run automatically and I've tested this on a fresh<br>> Bio-Linux 8 installation. To manually control it you can run "sudo<br>> stop<br>> galaxy" or "sudo start galaxy" but other ways of running the server<br>> might not work.<br>><br>> To see if files are missing please run:<br>><br>> sudo -u Debian-galaxy ls -l /usr/lib/galaxy-server --color=auto<br>><br>> Does anything show up in red? Can you please post the listing you<br>> get?<br>><br>> Cheers,<br>><br>> TIM<br>><br><br><br><br>Message: 2<br>Date: Wed, 15 Jul 2015 10:26:29 +0100<br>From: Tony Travis <<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>><br>To: <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>Subject: Re: [Bio-Linux] Galaxy on Bio-Linux 8 does not start.<br>'ExpatError'<br>Message-ID: <<a href="mailto:55A62745.8020706@abdn.ac.uk">55A62745.8020706@abdn.ac.uk</a>><br>Content-Type: text/plain; charset="windows-1252"<br><br>On 15/07/15 10:09, Julian Jaeger wrote:<br>> Hi everyone!<br>><br>> I just installed Bio-Linux 8, which has Galaxy on board. Unfortunatly<br>> Galaxy won't start.<br>><br>> Here is the recent traceback from the logfile:<br>> [...]<br><br>Hi, Julian.<br><br>How did you install Bio-Linux 8?<br><br>Galaxy is working fine for me either from the 'live' USB-stick or when<br>installed onto the hard disk. You might have problems if you upgraded an<br>existing system. Another thing to check is that your installation media<br>is free from errors (run check the media from the boot menu).<br><br>Bye,<br><br>Tony.<br><br><o:p></o:p></p></blockquote></div></div></body></html>