From juls.jaeger at gmx.de Wed Jul 15 05:09:14 2015 From: juls.jaeger at gmx.de (Julian Jaeger) Date: Wed, 15 Jul 2015 10:09:14 +0100 Subject: [Bio-Linux] Galaxy on Bio-Linux 8 does not start. 'ExpatError' Message-ID: <06a101d0bedd$ec23bf80$c46b3e80$@gmx.de> Hi everyone! I just installed Bio-Linux 8, which has Galaxy on board. Unfortunatly Galaxy won't start. Here is the recent traceback from the logfile: Traceback (most recent call last): File "/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/lib/galaxy-server/lib/galaxy/app.py", line 63, in __init__ self._configure_tool_data_tables( from_shed_config=False ) File "/usr/lib/galaxy-server/lib/galaxy/config.py", line 592, in _configure_tool_data_tables from_shed_config=from_shed_config ) File "/usr/lib/galaxy-server/lib/galaxy/tools/data/__init__.py", line 63, in load_from_config_file tree = util.parse_xml( filename ) File "/usr/lib/galaxy-server/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 584, in parse self._root = parser.close() File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Can anyone help, please? Many thanks , Julian -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Wed Jul 15 05:26:29 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 15 Jul 2015 10:26:29 +0100 Subject: [Bio-Linux] Galaxy on Bio-Linux 8 does not start. 'ExpatError' In-Reply-To: <06a101d0bedd$ec23bf80$c46b3e80$@gmx.de> References: <06a101d0bedd$ec23bf80$c46b3e80$@gmx.de> Message-ID: <55A62745.8020706@abdn.ac.uk> 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. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From jaeger.julian at gmx.net Wed Jul 15 05:41:21 2015 From: jaeger.julian at gmx.net (jaeger.julian at gmx.net) Date: Wed, 15 Jul 2015 10:41:21 +0100 Subject: [Bio-Linux] FW: Galaxy on Bio-Linux 8 does not start. 'ExpatError' Message-ID: <001101d0bee2$68e6d8f0$3ab48ad0$@gmx.net> Hi everyone! I just installed Bio-Linux 8. Unfortunatly Galaxy won't start. Here is the recent traceback from the logfile: Traceback (most recent call last): File "/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/lib/galaxy-server/lib/galaxy/app.py", line 63, in __init__ self._configure_tool_data_tables( from_shed_config=False ) File "/usr/lib/galaxy-server/lib/galaxy/config.py", line 592, in _configure_tool_data_tables from_shed_config=from_shed_config ) File "/usr/lib/galaxy-server/lib/galaxy/tools/data/__init__.py", line 63, in load_from_config_file tree = util.parse_xml( filename ) File "/usr/lib/galaxy-server/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 584, in parse self._root = parser.close() File "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtre e/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Can anyone help, please? Many thanks , Julian -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Jul 15 07:15:56 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 15 Jul 2015 12:15:56 +0100 Subject: [Bio-Linux] FW: Galaxy on Bio-Linux 8 does not start. 'ExpatError' In-Reply-To: <001101d0bee2$68e6d8f0$3ab48ad0$@gmx.net> References: <001101d0bee2$68e6d8f0$3ab48ad0$@gmx.net> Message-ID: <1436958956.5659.129.camel@wllt1771.nerc-wallingford.ac.uk> 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 On Wed, 2015-07-15 at 10:41 +0100, jaeger.julian at gmx.net wrote: > Hi everyone! > > I just installed Bio-Linux 8. Unfortunatly Galaxy won't start. > > Here is the recent traceback from the logfile: > > Traceback (most recent call last): > File "/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/buildapp.py", > line 39, in app_factory > app = UniverseApplication( global_conf = global_conf, **kwargs ) > File "/usr/lib/galaxy-server/lib/galaxy/app.py", line 63, in > __init__ > self._configure_tool_data_tables( from_shed_config=False ) > File "/usr/lib/galaxy-server/lib/galaxy/config.py", line 592, in > _configure_tool_data_tables > from_shed_config=from_shed_config ) > File "/usr/lib/galaxy-server/lib/galaxy/tools/data/__init__.py", > line 63, in load_from_config_file > tree = util.parse_xml( filename ) > File "/usr/lib/galaxy-server/lib/galaxy/util/__init__.py", line 154, > in parse_xml > tree = ElementTree.parse(fname) > File > "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse > tree.parse(source, parser) > File > "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 584, in parse > self._root = parser.close() > File > "/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 1251, in close > self._parser.Parse("", 1) # end of data > ExpatError: no element found: line 1, column 0 > > > > Can anyone help, please? > > > > Many thanks , Julian > > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From dksamuel2 at gmail.com Wed Jul 15 23:52:34 2015 From: dksamuel2 at gmail.com (Duleep Samuel) Date: Thu, 16 Jul 2015 09:22:34 +0530 Subject: [Bio-Linux] has anyone compiled Bio-linux to run on raspberry Pi 2 Message-ID: Sir/Madam,has anyone compiled Bio-linux to run on raspberry Pi 2, it will be so useful for teaching, Dr.D.K.Samuel, IIHR, Bangalore, India -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Jul 16 06:19:44 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 16 Jul 2015 11:19:44 +0100 Subject: [Bio-Linux] has anyone compiled Bio-linux to run on raspberry Pi 2 In-Reply-To: References: Message-ID: <1437041984.5477.26.camel@wllt1771.nerc-wallingford.ac.uk> Hi Dr. Samuel, Even better, there is a specific project for bioinformatics on the Pi which is focussed on teaching. You can find it here: http://eggg.st-andrews.ac.uk/4273pi/ I don't think they have a mailing list but I do know the lead developer, Daniel Barker, and he will be very happy to hear from you directly: db60 at st-andrews.ac.uk Best, TIM On Thu, 2015-07-16 at 09:22 +0530, Duleep Samuel wrote: > Sir/Madam,has anyone compiled Bio-linux to run on raspberry Pi 2, it > will be so useful for teaching, Dr.D.K.Samuel, IIHR, Bangalore, India > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From jaeger.julian at gmx.net Fri Jul 17 14:22:42 2015 From: jaeger.julian at gmx.net (jaeger.julian at gmx.net) Date: Fri, 17 Jul 2015 19:22:42 +0100 Subject: [Bio-Linux] Bio-Linux Digest, Vol 82, Issue 3 PROBLEM SOLVED -- Message-ID: <000a01d0c0bd$92836160$b78a2420$@gmx.net> 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 J?ger" [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 @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 wrote: > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > 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 > > To: Bio-Linux help and discussion > > 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 > > 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 > To: > Subject: Re: [Bio-Linux] Galaxy on Bio-Linux 8 does not start. 'ExpatError' Message-ID: <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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Jul 23 11:59:58 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 23 Jul 2015 16:59:58 +0100 Subject: [Bio-Linux] OpenSSH bug and SSH security in general Message-ID: <1437667198.14060.152.camel@wllt1771.nerc-wallingford.ac.uk> Hi All, A recently reported weakness in SSH can increase the vulnerability of Linux systems to brute-force password guessing attacks: http://www.itworld.com/article/2951494/bug-exposes-openssh-servers-to-bruteforce-password-guessing-attacks.html The good news is that the default configuration on Bio-Linux 8 does not allow this specific issue to be exploited, but it seems timely to remind/inform you of some security considerations regarding SSH. Having an intruder or bot on your system is very bad news indeed and a few minutes to consider security now could save you days of grief later. This does not really apply if you have Bio-Linux on a VM (VirtualBox), which is not externally accessible, but if you have the system fully installed please read on... 1) SSH server is enabled in Bio-Linux to allow remote login, file copying (SCP) and x2go functionality. Most people will need at least one of these, but if you don't you can choose to block SSH entirely. The simplest option is to go to Firewall Configuration under System Settings, then delete the pair of rules that start with the number 22. You can add these rules back at any time and SSH will be accessible again. You could also modify the rules to limit access by specific IP address. If you installed Bio-Linux on top of Ubuntu using the upgrade8.sh script you may not have a local firewall at all. You should consider enabling it by adding the "gufw" package, then turning it on under System Settings. Configuration with GUFW is very straightforward. 2) Check which users on your system have access via SSH. To do this you can run: getent group ssh If you see accounts listed which don't need remote SSH access you should disable them (eg. to disable ssh for user fred): sudo gpasswd -d fred ssh 3) Use secure passwords for all accounts, or even better disable password-based login via SSH and use cryptographic keys instead. There is a nicely written HOWTO here: https://kimmo.suominen.com/docs/ssh/ Note that if your client system is Windows, the PuTTYGen tool can do the job of ssh-keygen. If you have keys working, you can edit /etc/ssh/sshd_conf and set "PasswordAuthentication no" to go key-only. 4) If you have Bio-Linux on a laptop, remember that when you travel outside your home or office network you will not be protected by corporate firewalls etc., so this is a particular reason to consider how secure your system is. Consider using the internal firewall to block SSH when you are on the move and using public WiFi. 5) Some people recommend tools like fail2ban that try to detect and block intruders. I personally think these provide very limited protection and prone to locking you out of your own machine. Only consider this if key-based authentication and host whitelisting via the firewall settings are impractical for you. I hope this info is useful. Cheers, TIM -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tauqeer9 at gmail.com Mon Jul 27 21:39:31 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Mon, 27 Jul 2015 21:39:31 -0400 Subject: [Bio-Linux] Menu bar and Unity launcher disappeared Message-ID: Hi Tim I am using Biolinux8 as only OS on my machine. This morning I noticed that the menu bar and the side bar disappeared when I logged in through Ubuntu (default). The Ctrl+Alt+t command is also not working. However, I can access everything when I log in through Compiz, Metacity or MATE. Please help! Thanks Tauqeer -------------- next part -------------- An HTML attachment was scrubbed... URL: From tauqeer9 at gmail.com Tue Jul 28 10:52:08 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Tue, 28 Jul 2015 10:52:08 -0400 Subject: [Bio-Linux] Menu bar and Unity launcher disappeared Message-ID: Hi Tim I am using Biolinux8 as only OS on my machine. This morning I noticed that the menu bar and the side bar disappeared when I logged in through Ubuntu (default). The Ctrl+Alt+t command is also not working. However, I can access everything when I log in through Compiz, Metacity or MATE. Please help! Thanks Tauqeer -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Jul 28 11:01:23 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 28 Jul 2015 16:01:23 +0100 Subject: [Bio-Linux] Menu bar and Unity launcher disappeared In-Reply-To: References: Message-ID: <1438095683.5557.145.camel@wllt1771.nerc-wallingford.ac.uk> Hi, I've seen this a couple of times before. Assuming your system didn't fail part way through a package update it's normally due to a corrupted settings file in your home folder. To investigate, you can make a temporary folder and shunt all your dot files into it (don't delete the files - they have important application data in): $ mkdir ~/my_dot_files $ mv ~/.* ~/my_dot_files If you get an error about permissions, fix the permissions so all files can be moved. Then log out and back in. Does that fix it? If so, do "ls -A ~" to see what files and directories got recreated and just move back those that did not. An exception is that you should get a new ~/.local/share directory and you can restore the missing items from ~/my_dot_files/.local/share to get back those application settings too. Cheers, TIM On Mon, 2015-07-27 at 21:39 -0400, Tauqeer Alam wrote: > Hi Tim > > I am using Biolinux8 as only OS on my machine. This morning I noticed > that the menu bar and the side bar disappeared when I logged in > through Ubuntu (default). The Ctrl+Alt+t command is also not working. > However, I can access everything when I log in through Compiz, > Metacity or MATE. > > > Please help! > > > Thanks > > > Tauqeer > > > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tbooth at ceh.ac.uk Thu Jul 30 13:09:10 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 30 Jul 2015 18:09:10 +0100 Subject: [Bio-Linux] New QIIME 1.9.1 Message-ID: <1438276150.5557.335.camel@wllt1771.nerc-wallingford.ac.uk> Dear All, I've bumped QIIME up to the 1.9.1 bugfix release and also updated the "burrito" library used by QIIME under the hood. This fixes some important bugs documented here: https://github.com/biocore/qiime/blob/1.9.1/ChangeLog.md If you have used QIIME 1.9.0 on your data please check to see if any of these issues might have impacted your analysis and if you need to re-run anything. Also, there is a possibility this might fix the bug reported by Livio with corrupted BIOM files, though I'm still not sure what the actual cause of the issue was. Has anyone else made BIOM files they can't read or convert? I aspire to get all QIIME updates out to users within a month of release but due to unfortunate timing this one took more like two months. I hope the next one will reach you quicker. Best, TIM -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tauqeer9 at gmail.com Thu Jul 30 19:19:38 2015 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Thu, 30 Jul 2015 19:19:38 -0400 Subject: [Bio-Linux] Menu bar and Unity launcher disappeared In-Reply-To: <1438095683.5557.145.camel@wllt1771.nerc-wallingford.ac.uk> References: <1438095683.5557.145.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: Thanks Tim! This worked and I could fix the problem. The problem was with my ".profile" file. Really appreciate your help Best Tauqeer On Tue, Jul 28, 2015 at 11:01 AM, Tim Booth wrote: > Hi, > > I've seen this a couple of times before. Assuming your system didn't > fail part way through a package update it's normally due to a corrupted > settings file in your home folder. To investigate, you can make a > temporary folder and shunt all your dot files into it (don't delete the > files - they have important application data in): > > $ mkdir ~/my_dot_files > $ mv ~/.* ~/my_dot_files > > If you get an error about permissions, fix the permissions so all files > can be moved. > > Then log out and back in. Does that fix it? > > If so, do "ls -A ~" to see what files and directories got recreated and > just move back those that did not. An exception is that you should get > a new ~/.local/share directory and you can restore the missing items > from ~/my_dot_files/.local/share to get back those application settings > too. > > Cheers, > > TIM > > On Mon, 2015-07-27 at 21:39 -0400, Tauqeer Alam wrote: > > Hi Tim > > > > I am using Biolinux8 as only OS on my machine. This morning I noticed > > that the menu bar and the side bar disappeared when I logged in > > through Ubuntu (default). The Ctrl+Alt+t command is also not working. > > However, I can access everything when I log in through Compiz, > > Metacity or MATE. > > > > > > Please help! > > > > > > Thanks > > > > > > Tauqeer > > > > > > > > > > > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- > Tim Booth > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://environmentalomics.org/bio-linux > +44 1491 69 2297 > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mictadlo at gmail.com Thu Jul 30 21:12:03 2015 From: mictadlo at gmail.com (Mic) Date: Fri, 31 Jul 2015 11:12:03 +1000 Subject: [Bio-Linux] Galaxy: How to install the same tools like usegalaxy.org has Message-ID: Hello, What is the best way to install the same tools like usegalaxy.org has? I found also an ansible-playbook here ( https://github.com/galaxyproject/usegalaxy-playbook ), but I am not sure whether it is compatible with Bio-Linux and I have never used ansible before. Furthermore, I found this xml file ( https://github.com/galaxyproject/usegalaxy-playbook/blob/664d38a60d87a4cd8f697d5ecd0fd062b238bc75/files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml ) which contains all tools on usegalaxy.org, but I do not how to use it in order to install all tools on Bio-Linux Galaxy. Thank you in advance. Mic -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdjukic1 at gwdg.de Fri Jul 31 04:15:01 2015 From: mdjukic1 at gwdg.de (Marvin Djukic) Date: Fri, 31 Jul 2015 10:15:01 +0200 Subject: [Bio-Linux] qiime filter_fasta.py problem Message-ID: <55BB2E85.8040505@gwdg.de> Dear Bio-Linux Users, maybe you're able to help me with the following problem: Anytime I try to use "*filter_fasta.py*" (*qiime package*) I get an error message. qiime > filter_fasta.py -f data.fas -o test -s list Traceback (most recent call last): File "/usr/local/bin/filter_fasta.py", line 183, in main() File "/usr/local/bin/filter_fasta.py", line 180, in main negate) File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp return filter_fasta(input_seqs,output_f,seqs_to_keep,negate) File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352, in filter_fasta for seq_id, seq in parse_fasta(input_seqs_f): File "/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py", line 136, in parse_fasta for rec in finder(infile): File "/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line 150, in parser line = constructor(l) TypeError: descriptor 'strip' requires a 'str' object but received a 'tuple' I'm not sure if it is really a qiime-related error. Maybe something went wrong with the installation. However, I already re-installed the whole qiime package once and there seems to be no problem (output from "print_qiime_config_all" see below). Is there anyone who is able to help me with this issue? Thanks a lot, best regards, Marvin print_qiime_config_all: System information ================== Platform: linux2 Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] Python executable: /usr/bin/python QIIME default reference information =================================== For details on what files are used as QIIME's default references, see here: https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1 Dependency versions =================== QIIME library version: 1.9.0 QIIME script version: 1.9.0+dfsg-0biolinux5 qiime-default-reference version: 0.1.1 NumPy version: 1.8.2 SciPy version: 0.13.3 pandas version: 0.13.1 matplotlib version: 1.3.1 biom-format version: 2.1.4 h5py version: 2.2.1 (HDF5 version: 1.8.11) qcli version: 0.1.0 pyqi version: 0.3.2 scikit-bio version: 0.2.3 PyNAST version: 1.2.2 Emperor version: 0.9.51 burrito version: 0.9.0 burrito-fillings version: Installed. sortmerna version: SortMeRNA version 2.0, 29/11/2014 sumaclust version: SUMACLUST Version 1.0.01 swarm version: Swarm 1.2.20 [Feb 1 2015 09:42:15] gdata: Not installed. QIIME config values =================== For definitions of these settings and to learn how to configure QIIME, see here: http://qiime.org/install/qiime_config.html http://qiime.org/tutorials/parallel_qiime.html blastmat_dir: /usr/share/ncbi/data cluster_jobs_fp: None pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta jobs_to_start: 1 pynast_template_alignment_blastdb: None qiime_scripts_dir: /usr/lib/qiime/bin/ working_dir: . pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed python_exe_fp: python temp_dir: /tmp assign_taxonomy_reference_seqs_fp: # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta blastall_fp: blastall seconds_to_sleep: 60 assign_taxonomy_id_to_taxonomy_fp: # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt QIIME base install test results =============================== ......... ---------------------------------------------------------------------- Ran 9 tests in 0.027s OK Here are the versions of the packages that QIIME depends on as reported by the system package manager: ampliconnoise : 1.29-2 blast2 : 1:2.2.26.20120620-7 bwa : 0.7.12-0biolinux1 cd-hit : 4.6.1-2012-08-27-2 chimeraslayer : 20101212+dfsg-1 clearcut : 1.0.9-0biolinux1.1 clustalw : 2.1+lgpl-4 ea-utils : 1.1.2+dfsg-1biolinux1 emperor : 0.9.51-0biolinux1 fasttree : 2.1.7-1biolinux1.1 infernal : 1.1.1-2ubuntu1 mafft : 7.215-0biolinux1 mothur : 1.34.4+repack-0biolinux1 muscle : 1:3.8.31-1 parsinsert : 1.04-1biolinux1.1 pynast : 1.2.2-0biolinux1.1 python : 2.7.5-5ubuntu3 python-biom-format : 2.1.4-0biolinux2 python-burrito : 0.9.0-0biolinux3 python-burrito-fillings : 0.1.0-0biolinux4 python-cogent : 1.5.3-2biolinux2 python-matplotlib : 1.3.1-1ubuntu5 python-mpi4py : 1.3.1+hg20131106-1build3 python-numpy : 1:1.8.2-0ubuntu0.1 python-pandas : 0.13.1-2ubuntu2 python-qcli : 0.1.0-1 python : 2.7.5-5ubuntu3 qiime-data : 1.9.0+dfsg-0biolinux5 qiime-default-reference : 0.1.1-0biolinux2 r-cran-optparse : 1.3.0-1cran1ppa0 raxml : 8.0.26-0biolinux1 rdp-classifier : 2.10.2+dfsg-0biolinux1 seqprep : 1.1-0biolinux2 sortmerna : 2.0-0biolinux1 sumatra : 1.0.01-0ubuntu1 swarm : 1.2.20-0biolinux1 vsearch : 1.1.1.nodata-0biolinux1 OK -- Dipl. Biol. Marvin Djukic Georg-August Universit?t G?ttingen Institut f?r Mikrobiologie und Genetik G?ttingen Genomics Laboratory Grisebachstra?e 8 37077 G?ttingen Germany Tel. 0049-(0)551-39-33843 Mobil: 0176-45743636 E-Mail: mdjukic1 at gwdg.de http://appmibio.uni-goettingen.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Fri Jul 31 07:02:35 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 31 Jul 2015 12:02:35 +0100 Subject: [Bio-Linux] qiime filter_fasta.py problem In-Reply-To: <55BB2E85.8040505@gwdg.de> References: <55BB2E85.8040505@gwdg.de> Message-ID: <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> Hi Marvin, The mailing list server says you are not subscribed to the list. Maybe you just signed up on a slightly different address, which is fine, otherwise please check or you might not see all the replies. Did you see my announcement on the list yesterday of QIIME 1.9.1? Please try the updated version, but I don't think it will solve your problem. My best guess is that you have some issue with your FASTA file that is upsetting the parser. To be sure, try running the filter with a small FASTA file like /usr/local/bioinf/sampledata/nucleotide_seqs/multiple_seqs.fasta This should definitely work. Cheers, TIM On Fri, 2015-07-31 at 10:15 +0200, Marvin Djukic wrote: > Dear Bio-Linux Users, > > maybe you're able to help me with the following problem: > Anytime I try to use "filter_fasta.py" (qiime package) I get an error > message. > > qiime > filter_fasta.py -f data.fas -o test -s > list > Traceback (most recent call last): > File "/usr/local/bin/filter_fasta.py", line 183, in > main() > File "/usr/local/bin/filter_fasta.py", line 180, in main > negate) > File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp > return filter_fasta(input_seqs,output_f,seqs_to_keep,negate) > File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352, > in filter_fasta > for seq_id, seq in parse_fasta(input_seqs_f): > File > "/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py", > line 136, in parse_fasta > for rec in finder(infile): > File > "/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line > 150, in parser > line = constructor(l) > TypeError: descriptor 'strip' requires a 'str' object but received a > 'tuple' > > I'm not sure if it is really a qiime-related error. Maybe something > went wrong with the installation. However, I already re-installed the > whole qiime package once and there seems to be no problem (output from > "print_qiime_config_all" see below). > > Is there anyone who is able to help me with this issue? > > Thanks a lot, > > best regards, > Marvin > > > > > print_qiime_config_all: > System information > ================== > Platform: linux2 > Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC > 4.8.2] > Python executable: /usr/bin/python > > QIIME default reference information > =================================== > For details on what files are used as QIIME's default references, see > here: > https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1 > > Dependency versions > =================== > QIIME library version: 1.9.0 > QIIME script version: 1.9.0+dfsg-0biolinux5 > qiime-default-reference version: 0.1.1 > NumPy version: 1.8.2 > SciPy version: 0.13.3 > pandas version: 0.13.1 > matplotlib version: 1.3.1 > biom-format version: 2.1.4 > h5py version: 2.2.1 (HDF5 version: 1.8.11) > qcli version: 0.1.0 > pyqi version: 0.3.2 > scikit-bio version: 0.2.3 > PyNAST version: 1.2.2 > Emperor version: 0.9.51 > burrito version: 0.9.0 > burrito-fillings version: Installed. > sortmerna version: SortMeRNA version 2.0, 29/11/2014 > sumaclust version: SUMACLUST Version 1.0.01 > swarm version: Swarm 1.2.20 [Feb 1 2015 > 09:42:15] > gdata: Not installed. > > QIIME config values > =================== > For definitions of these settings and to learn how to configure QIIME, > see here: > http://qiime.org/install/qiime_config.html > http://qiime.org/tutorials/parallel_qiime.html > > blastmat_dir: /usr/share/ncbi/data > cluster_jobs_fp: None > > pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta > jobs_to_start: 1 > pynast_template_alignment_blastdb: None > qiime_scripts_dir: /usr/lib/qiime/bin/ > working_dir: . > > pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed > python_exe_fp: python > temp_dir: /tmp > assign_taxonomy_reference_seqs_fp: > # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta > blastall_fp: blastall > seconds_to_sleep: 60 > assign_taxonomy_id_to_taxonomy_fp: > # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt > > QIIME base install test results > =============================== > ......... > ---------------------------------------------------------------------- > Ran 9 tests in 0.027s > > OK > > Here are the versions of the packages that QIIME depends on as > reported by > the system package manager: > > ampliconnoise : 1.29-2 > blast2 : 1:2.2.26.20120620-7 > bwa : 0.7.12-0biolinux1 > cd-hit : 4.6.1-2012-08-27-2 > chimeraslayer : 20101212+dfsg-1 > clearcut : 1.0.9-0biolinux1.1 > clustalw : 2.1+lgpl-4 > ea-utils : 1.1.2+dfsg-1biolinux1 > emperor : 0.9.51-0biolinux1 > fasttree : 2.1.7-1biolinux1.1 > infernal : 1.1.1-2ubuntu1 > mafft : 7.215-0biolinux1 > mothur : 1.34.4+repack-0biolinux1 > muscle : 1:3.8.31-1 > parsinsert : 1.04-1biolinux1.1 > pynast : 1.2.2-0biolinux1.1 > python : 2.7.5-5ubuntu3 > python-biom-format : 2.1.4-0biolinux2 > python-burrito : 0.9.0-0biolinux3 > python-burrito-fillings : 0.1.0-0biolinux4 > python-cogent : 1.5.3-2biolinux2 > python-matplotlib : 1.3.1-1ubuntu5 > python-mpi4py : 1.3.1+hg20131106-1build3 > python-numpy : 1:1.8.2-0ubuntu0.1 > python-pandas : 0.13.1-2ubuntu2 > python-qcli : 0.1.0-1 > python : 2.7.5-5ubuntu3 > qiime-data : 1.9.0+dfsg-0biolinux5 > qiime-default-reference : 0.1.1-0biolinux2 > r-cran-optparse : 1.3.0-1cran1ppa0 > raxml : 8.0.26-0biolinux1 > rdp-classifier : 2.10.2+dfsg-0biolinux1 > seqprep : 1.1-0biolinux2 > sortmerna : 2.0-0biolinux1 > sumatra : 1.0.01-0ubuntu1 > swarm : 1.2.20-0biolinux1 > vsearch : 1.1.1.nodata-0biolinux1 > > OK > > > -- > Dipl. Biol. Marvin Djukic > Georg-August Universit?t G?ttingen > Institut f?r Mikrobiologie und Genetik > > G?ttingen Genomics Laboratory > Grisebachstra?e 8 > 37077 G?ttingen > Germany > > Tel. 0049-(0)551-39-33843 > Mobil: 0176-45743636 > E-Mail: mdjukic1 at gwdg.de > http://appmibio.uni-goettingen.de > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From mdjukic1 at gwdg.de Fri Jul 31 07:39:12 2015 From: mdjukic1 at gwdg.de (Marvin Djukic) Date: Fri, 31 Jul 2015 13:39:12 +0200 Subject: [Bio-Linux] qiime filter_fasta.py problem In-Reply-To: <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> References: <55BB2E85.8040505@gwdg.de> <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <55BB5E60.8090209@gwdg.de> Hi Tim, thanks for your reply. (Now I should be subscribed to the list.) I updated Qiime to 1.9.1, but the error is still exactly the same. I'm also *not**able to run filter_fasta.py with the sample data set*. Same error. Maybe someone else has an idea. Don't know what to change/do at the moment. Thanks a lot, regards, Marvin On 31.07.2015 13:02, Tim Booth wrote: > Hi Marvin, > > The mailing list server says you are not subscribed to the list. Maybe > you just signed up on a slightly different address, which is fine, > otherwise please check or you might not see all the replies. > > Did you see my announcement on the list yesterday of QIIME 1.9.1? > Please try the updated version, but I don't think it will solve your > problem. My best guess is that you have some issue with your FASTA file > that is upsetting the parser. > > To be sure, try running the filter with a small FASTA file like > > /usr/local/bioinf/sampledata/nucleotide_seqs/multiple_seqs.fasta > > This should definitely work. > > Cheers, > > TIM > > On Fri, 2015-07-31 at 10:15 +0200, Marvin Djukic wrote: >> Dear Bio-Linux Users, >> >> maybe you're able to help me with the following problem: >> Anytime I try to use "filter_fasta.py" (qiime package) I get an error >> message. >> >> qiime > filter_fasta.py -f data.fas -o test -s >> list >> Traceback (most recent call last): >> File "/usr/local/bin/filter_fasta.py", line 183, in >> main() >> File "/usr/local/bin/filter_fasta.py", line 180, in main >> negate) >> File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp >> return filter_fasta(input_seqs,output_f,seqs_to_keep,negate) >> File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352, >> in filter_fasta >> for seq_id, seq in parse_fasta(input_seqs_f): >> File >> "/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py", >> line 136, in parse_fasta >> for rec in finder(infile): >> File >> "/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line >> 150, in parser >> line = constructor(l) >> TypeError: descriptor 'strip' requires a 'str' object but received a >> 'tuple' >> >> I'm not sure if it is really a qiime-related error. Maybe something >> went wrong with the installation. However, I already re-installed the >> whole qiime package once and there seems to be no problem (output from >> "print_qiime_config_all" see below). >> >> Is there anyone who is able to help me with this issue? >> >> Thanks a lot, >> >> best regards, >> Marvin >> >> >> >> >> print_qiime_config_all: >> System information >> ================== >> Platform: linux2 >> Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC >> 4.8.2] >> Python executable: /usr/bin/python >> >> QIIME default reference information >> =================================== >> For details on what files are used as QIIME's default references, see >> here: >> https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1 >> >> Dependency versions >> =================== >> QIIME library version: 1.9.0 >> QIIME script version: 1.9.0+dfsg-0biolinux5 >> qiime-default-reference version: 0.1.1 >> NumPy version: 1.8.2 >> SciPy version: 0.13.3 >> pandas version: 0.13.1 >> matplotlib version: 1.3.1 >> biom-format version: 2.1.4 >> h5py version: 2.2.1 (HDF5 version: 1.8.11) >> qcli version: 0.1.0 >> pyqi version: 0.3.2 >> scikit-bio version: 0.2.3 >> PyNAST version: 1.2.2 >> Emperor version: 0.9.51 >> burrito version: 0.9.0 >> burrito-fillings version: Installed. >> sortmerna version: SortMeRNA version 2.0, 29/11/2014 >> sumaclust version: SUMACLUST Version 1.0.01 >> swarm version: Swarm 1.2.20 [Feb 1 2015 >> 09:42:15] >> gdata: Not installed. >> >> QIIME config values >> =================== >> For definitions of these settings and to learn how to configure QIIME, >> see here: >> http://qiime.org/install/qiime_config.html >> http://qiime.org/tutorials/parallel_qiime.html >> >> blastmat_dir: /usr/share/ncbi/data >> cluster_jobs_fp: None >> >> pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta >> jobs_to_start: 1 >> pynast_template_alignment_blastdb: None >> qiime_scripts_dir: /usr/lib/qiime/bin/ >> working_dir: . >> >> pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed >> python_exe_fp: python >> temp_dir: /tmp >> assign_taxonomy_reference_seqs_fp: >> # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta >> blastall_fp: blastall >> seconds_to_sleep: 60 >> assign_taxonomy_id_to_taxonomy_fp: >> # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt >> >> QIIME base install test results >> =============================== >> ......... >> ---------------------------------------------------------------------- >> Ran 9 tests in 0.027s >> >> OK >> >> Here are the versions of the packages that QIIME depends on as >> reported by >> the system package manager: >> >> ampliconnoise : 1.29-2 >> blast2 : 1:2.2.26.20120620-7 >> bwa : 0.7.12-0biolinux1 >> cd-hit : 4.6.1-2012-08-27-2 >> chimeraslayer : 20101212+dfsg-1 >> clearcut : 1.0.9-0biolinux1.1 >> clustalw : 2.1+lgpl-4 >> ea-utils : 1.1.2+dfsg-1biolinux1 >> emperor : 0.9.51-0biolinux1 >> fasttree : 2.1.7-1biolinux1.1 >> infernal : 1.1.1-2ubuntu1 >> mafft : 7.215-0biolinux1 >> mothur : 1.34.4+repack-0biolinux1 >> muscle : 1:3.8.31-1 >> parsinsert : 1.04-1biolinux1.1 >> pynast : 1.2.2-0biolinux1.1 >> python : 2.7.5-5ubuntu3 >> python-biom-format : 2.1.4-0biolinux2 >> python-burrito : 0.9.0-0biolinux3 >> python-burrito-fillings : 0.1.0-0biolinux4 >> python-cogent : 1.5.3-2biolinux2 >> python-matplotlib : 1.3.1-1ubuntu5 >> python-mpi4py : 1.3.1+hg20131106-1build3 >> python-numpy : 1:1.8.2-0ubuntu0.1 >> python-pandas : 0.13.1-2ubuntu2 >> python-qcli : 0.1.0-1 >> python : 2.7.5-5ubuntu3 >> qiime-data : 1.9.0+dfsg-0biolinux5 >> qiime-default-reference : 0.1.1-0biolinux2 >> r-cran-optparse : 1.3.0-1cran1ppa0 >> raxml : 8.0.26-0biolinux1 >> rdp-classifier : 2.10.2+dfsg-0biolinux1 >> seqprep : 1.1-0biolinux2 >> sortmerna : 2.0-0biolinux1 >> sumatra : 1.0.01-0ubuntu1 >> swarm : 1.2.20-0biolinux1 >> vsearch : 1.1.1.nodata-0biolinux1 >> >> OK >> >> >> -- >> Dipl. Biol. Marvin Djukic >> Georg-August Universit?t G?ttingen >> Institut f?r Mikrobiologie und Genetik >> >> G?ttingen Genomics Laboratory >> Grisebachstra?e 8 >> 37077 G?ttingen >> Germany >> >> Tel. 0049-(0)551-39-33843 >> Mobil: 0176-45743636 >> E-Mail: mdjukic1 at gwdg.de >> http://appmibio.uni-goettingen.de >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Dipl. Biol. Marvin Djukic Georg-August Universit?t G?ttingen Institut f?r Mikrobiologie und Genetik G?ttingen Genomics Laboratory Grisebachstra?e 8 37077 G?ttingen Germany Tel. 0049-(0)551-39-33843 Mobil: 0176-45743636 E-Mail: mdjukic1 at gwdg.de http://appmibio.uni-goettingen.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Fri Jul 31 08:21:36 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 31 Jul 2015 13:21:36 +0100 Subject: [Bio-Linux] qiime filter_fasta.py problem In-Reply-To: <55BB5E60.8090209@gwdg.de> References: <55BB2E85.8040505@gwdg.de> <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> <55BB5E60.8090209@gwdg.de> Message-ID: <1438345296.5557.404.camel@wllt1771.nerc-wallingford.ac.uk> Hi Marvin, OK, just had a second look at your error and it says: ... "/usr/local/bin/filter_fasta.py" ... This is not part of the QIIME package. The program should be: /usr/lib/qiime/bin/filter_fasta.py So it looks like you have some rogue QIIME scripts on your system. Possibly at some point you tried to install QIIME using the "pip install ..." mechanism? Please try removing /usr/local/bin/filter_fasta.py. In fact, unless you know you have explicitly installed Python scripts into /usr/local/bin it is safe to get rid of them all: sudo rm /usr/local/bin/*.py Does that fix it? Cheers, TIM > I updated Qiime to 1.9.1, but the error is still exactly the same. I'm > also not able to run filter_fasta.py with the sample data set. Same > error. > Maybe someone else has an idea. Don't know what to change/do at the > moment. > > Thanks a lot, > regards, > Marvin > > > On 31.07.2015 13:02, Tim Booth wrote: > > > Hi Marvin, > > > > The mailing list server says you are not subscribed to the list. Maybe > > you just signed up on a slightly different address, which is fine, > > otherwise please check or you might not see all the replies. > > > > Did you see my announcement on the list yesterday of QIIME 1.9.1? > > Please try the updated version, but I don't think it will solve your > > problem. My best guess is that you have some issue with your FASTA file > > that is upsetting the parser. > > > > To be sure, try running the filter with a small FASTA file like > > > > /usr/local/bioinf/sampledata/nucleotide_seqs/multiple_seqs.fasta > > > > This should definitely work. > > > > Cheers, > > > > TIM > > > > On Fri, 2015-07-31 at 10:15 +0200, Marvin Djukic wrote: > > > Dear Bio-Linux Users, > > > > > > maybe you're able to help me with the following problem: > > > Anytime I try to use "filter_fasta.py" (qiime package) I get an error > > > message. > > > > > > qiime > filter_fasta.py -f data.fas -o test -s > > > list > > > Traceback (most recent call last): > > > File "/usr/local/bin/filter_fasta.py", line 183, in > > > main() > > > File "/usr/local/bin/filter_fasta.py", line 180, in main > > > negate) > > > File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp > > > return filter_fasta(input_seqs,output_f,seqs_to_keep,negate) > > > File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352, > > > in filter_fasta > > > for seq_id, seq in parse_fasta(input_seqs_f): > > > File > > > "/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py", > > > line 136, in parse_fasta > > > for rec in finder(infile): > > > File > > > "/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line > > > 150, in parser > > > line = constructor(l) > > > TypeError: descriptor 'strip' requires a 'str' object but received a > > > 'tuple' > > > > > > I'm not sure if it is really a qiime-related error. Maybe something > > > went wrong with the installation. However, I already re-installed the > > > whole qiime package once and there seems to be no problem (output from > > > "print_qiime_config_all" see below). > > > > > > Is there anyone who is able to help me with this issue? > > > > > > Thanks a lot, > > > > > > best regards, > > > Marvin > > > > > > > > > > > > > > > print_qiime_config_all: > > > System information > > > ================== > > > Platform: linux2 > > > Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC > > > 4.8.2] > > > Python executable: /usr/bin/python > > > > > > QIIME default reference information > > > =================================== > > > For details on what files are used as QIIME's default references, see > > > here: > > > https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1 > > > > > > Dependency versions > > > =================== > > > QIIME library version: 1.9.0 > > > QIIME script version: 1.9.0+dfsg-0biolinux5 > > > qiime-default-reference version: 0.1.1 > > > NumPy version: 1.8.2 > > > SciPy version: 0.13.3 > > > pandas version: 0.13.1 > > > matplotlib version: 1.3.1 > > > biom-format version: 2.1.4 > > > h5py version: 2.2.1 (HDF5 version: 1.8.11) > > > qcli version: 0.1.0 > > > pyqi version: 0.3.2 > > > scikit-bio version: 0.2.3 > > > PyNAST version: 1.2.2 > > > Emperor version: 0.9.51 > > > burrito version: 0.9.0 > > > burrito-fillings version: Installed. > > > sortmerna version: SortMeRNA version 2.0, 29/11/2014 > > > sumaclust version: SUMACLUST Version 1.0.01 > > > swarm version: Swarm 1.2.20 [Feb 1 2015 > > > 09:42:15] > > > gdata: Not installed. > > > > > > QIIME config values > > > =================== > > > For definitions of these settings and to learn how to configure QIIME, > > > see here: > > > http://qiime.org/install/qiime_config.html > > > http://qiime.org/tutorials/parallel_qiime.html > > > > > > blastmat_dir: /usr/share/ncbi/data > > > cluster_jobs_fp: None > > > > > > pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta > > > jobs_to_start: 1 > > > pynast_template_alignment_blastdb: None > > > qiime_scripts_dir: /usr/lib/qiime/bin/ > > > working_dir: . > > > > > > pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed > > > python_exe_fp: python > > > temp_dir: /tmp > > > assign_taxonomy_reference_seqs_fp: > > > # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta > > > blastall_fp: blastall > > > seconds_to_sleep: 60 > > > assign_taxonomy_id_to_taxonomy_fp: > > > # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt > > > > > > QIIME base install test results > > > =============================== > > > ......... > > > ---------------------------------------------------------------------- > > > Ran 9 tests in 0.027s > > > > > > OK > > > > > > Here are the versions of the packages that QIIME depends on as > > > reported by > > > the system package manager: > > > > > > ampliconnoise : 1.29-2 > > > blast2 : 1:2.2.26.20120620-7 > > > bwa : 0.7.12-0biolinux1 > > > cd-hit : 4.6.1-2012-08-27-2 > > > chimeraslayer : 20101212+dfsg-1 > > > clearcut : 1.0.9-0biolinux1.1 > > > clustalw : 2.1+lgpl-4 > > > ea-utils : 1.1.2+dfsg-1biolinux1 > > > emperor : 0.9.51-0biolinux1 > > > fasttree : 2.1.7-1biolinux1.1 > > > infernal : 1.1.1-2ubuntu1 > > > mafft : 7.215-0biolinux1 > > > mothur : 1.34.4+repack-0biolinux1 > > > muscle : 1:3.8.31-1 > > > parsinsert : 1.04-1biolinux1.1 > > > pynast : 1.2.2-0biolinux1.1 > > > python : 2.7.5-5ubuntu3 > > > python-biom-format : 2.1.4-0biolinux2 > > > python-burrito : 0.9.0-0biolinux3 > > > python-burrito-fillings : 0.1.0-0biolinux4 > > > python-cogent : 1.5.3-2biolinux2 > > > python-matplotlib : 1.3.1-1ubuntu5 > > > python-mpi4py : 1.3.1+hg20131106-1build3 > > > python-numpy : 1:1.8.2-0ubuntu0.1 > > > python-pandas : 0.13.1-2ubuntu2 > > > python-qcli : 0.1.0-1 > > > python : 2.7.5-5ubuntu3 > > > qiime-data : 1.9.0+dfsg-0biolinux5 > > > qiime-default-reference : 0.1.1-0biolinux2 > > > r-cran-optparse : 1.3.0-1cran1ppa0 > > > raxml : 8.0.26-0biolinux1 > > > rdp-classifier : 2.10.2+dfsg-0biolinux1 > > > seqprep : 1.1-0biolinux2 > > > sortmerna : 2.0-0biolinux1 > > > sumatra : 1.0.01-0ubuntu1 > > > swarm : 1.2.20-0biolinux1 > > > vsearch : 1.1.1.nodata-0biolinux1 > > > > > > OK > > > > > > > > -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From mdjukic1 at gwdg.de Fri Jul 31 08:26:06 2015 From: mdjukic1 at gwdg.de (Marvin Djukic) Date: Fri, 31 Jul 2015 14:26:06 +0200 Subject: [Bio-Linux] qiime filter_fasta.py problem In-Reply-To: <1438345296.5557.404.camel@wllt1771.nerc-wallingford.ac.uk> References: <55BB2E85.8040505@gwdg.de> <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> <55BB5E60.8090209@gwdg.de> <1438345296.5557.404.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <55BB695E.2040208@gwdg.de> Hi Tim, You're right - I guess I manually installed it the wrong way and didn't delete all "old" files. And yes, that fixed it. MANY many thanks. Regards, Marvin On 31.07.2015 14:21, Tim Booth wrote: > Hi Marvin, > > OK, just had a second look at your error and it says: > > ... "/usr/local/bin/filter_fasta.py" ... > > This is not part of the QIIME package. The program should be: > > /usr/lib/qiime/bin/filter_fasta.py > > So it looks like you have some rogue QIIME scripts on your system. > Possibly at some point you tried to install QIIME using the "pip > install ..." mechanism? > > Please try removing /usr/local/bin/filter_fasta.py. In fact, unless you > know you have explicitly installed Python scripts into /usr/local/bin it > is safe to get rid of them all: > > sudo rm /usr/local/bin/*.py > > Does that fix it? > > Cheers, > > TIM > >> I updated Qiime to 1.9.1, but the error is still exactly the same. I'm >> also not able to run filter_fasta.py with the sample data set. Same >> error. >> Maybe someone else has an idea. Don't know what to change/do at the >> moment. >> >> Thanks a lot, >> regards, >> Marvin >> >> >> On 31.07.2015 13:02, Tim Booth wrote: >> >>> Hi Marvin, >>> >>> The mailing list server says you are not subscribed to the list. Maybe >>> you just signed up on a slightly different address, which is fine, >>> otherwise please check or you might not see all the replies. >>> >>> Did you see my announcement on the list yesterday of QIIME 1.9.1? >>> Please try the updated version, but I don't think it will solve your >>> problem. My best guess is that you have some issue with your FASTA file >>> that is upsetting the parser. >>> >>> To be sure, try running the filter with a small FASTA file like >>> >>> /usr/local/bioinf/sampledata/nucleotide_seqs/multiple_seqs.fasta >>> >>> This should definitely work. >>> >>> Cheers, >>> >>> TIM >>> >>> On Fri, 2015-07-31 at 10:15 +0200, Marvin Djukic wrote: >>>> Dear Bio-Linux Users, >>>> >>>> maybe you're able to help me with the following problem: >>>> Anytime I try to use "filter_fasta.py" (qiime package) I get an error >>>> message. >>>> >>>> qiime > filter_fasta.py -f data.fas -o test -s >>>> list >>>> Traceback (most recent call last): >>>> File "/usr/local/bin/filter_fasta.py", line 183, in >>>> main() >>>> File "/usr/local/bin/filter_fasta.py", line 180, in main >>>> negate) >>>> File "/usr/local/bin/filter_fasta.py", line 84, in filter_fasta_fp >>>> return filter_fasta(input_seqs,output_f,seqs_to_keep,negate) >>>> File "/usr/lib/python2.7/dist-packages/qiime/filter.py", line 352, >>>> in filter_fasta >>>> for seq_id, seq in parse_fasta(input_seqs_f): >>>> File >>>> "/usr/lib/python2.7/dist-packages/skbio/parse/sequences/fasta.py", >>>> line 136, in parse_fasta >>>> for rec in finder(infile): >>>> File >>>> "/usr/lib/python2.7/dist-packages/skbio/parse/record_finder.py", line >>>> 150, in parser >>>> line = constructor(l) >>>> TypeError: descriptor 'strip' requires a 'str' object but received a >>>> 'tuple' >>>> >>>> I'm not sure if it is really a qiime-related error. Maybe something >>>> went wrong with the installation. However, I already re-installed the >>>> whole qiime package once and there seems to be no problem (output from >>>> "print_qiime_config_all" see below). >>>> >>>> Is there anyone who is able to help me with this issue? >>>> >>>> Thanks a lot, >>>> >>>> best regards, >>>> Marvin >>>> >>>> >>>> >>>> >>>> print_qiime_config_all: >>>> System information >>>> ================== >>>> Platform: linux2 >>>> Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC >>>> 4.8.2] >>>> Python executable: /usr/bin/python >>>> >>>> QIIME default reference information >>>> =================================== >>>> For details on what files are used as QIIME's default references, see >>>> here: >>>> https://github.com/biocore/qiime-default-reference/releases/tag/0.1.1 >>>> >>>> Dependency versions >>>> =================== >>>> QIIME library version: 1.9.0 >>>> QIIME script version: 1.9.0+dfsg-0biolinux5 >>>> qiime-default-reference version: 0.1.1 >>>> NumPy version: 1.8.2 >>>> SciPy version: 0.13.3 >>>> pandas version: 0.13.1 >>>> matplotlib version: 1.3.1 >>>> biom-format version: 2.1.4 >>>> h5py version: 2.2.1 (HDF5 version: 1.8.11) >>>> qcli version: 0.1.0 >>>> pyqi version: 0.3.2 >>>> scikit-bio version: 0.2.3 >>>> PyNAST version: 1.2.2 >>>> Emperor version: 0.9.51 >>>> burrito version: 0.9.0 >>>> burrito-fillings version: Installed. >>>> sortmerna version: SortMeRNA version 2.0, 29/11/2014 >>>> sumaclust version: SUMACLUST Version 1.0.01 >>>> swarm version: Swarm 1.2.20 [Feb 1 2015 >>>> 09:42:15] >>>> gdata: Not installed. >>>> >>>> QIIME config values >>>> =================== >>>> For definitions of these settings and to learn how to configure QIIME, >>>> see here: >>>> http://qiime.org/install/qiime_config.html >>>> http://qiime.org/tutorials/parallel_qiime.html >>>> >>>> blastmat_dir: /usr/share/ncbi/data >>>> cluster_jobs_fp: None >>>> >>>> pick_otus_reference_seqs_fp: /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta >>>> jobs_to_start: 1 >>>> pynast_template_alignment_blastdb: None >>>> qiime_scripts_dir: /usr/lib/qiime/bin/ >>>> working_dir: . >>>> >>>> pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed >>>> python_exe_fp: python >>>> temp_dir: /tmp >>>> assign_taxonomy_reference_seqs_fp: >>>> # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta >>>> blastall_fp: blastall >>>> seconds_to_sleep: 60 >>>> assign_taxonomy_id_to_taxonomy_fp: >>>> # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt >>>> >>>> QIIME base install test results >>>> =============================== >>>> ......... >>>> ---------------------------------------------------------------------- >>>> Ran 9 tests in 0.027s >>>> >>>> OK >>>> >>>> Here are the versions of the packages that QIIME depends on as >>>> reported by >>>> the system package manager: >>>> >>>> ampliconnoise : 1.29-2 >>>> blast2 : 1:2.2.26.20120620-7 >>>> bwa : 0.7.12-0biolinux1 >>>> cd-hit : 4.6.1-2012-08-27-2 >>>> chimeraslayer : 20101212+dfsg-1 >>>> clearcut : 1.0.9-0biolinux1.1 >>>> clustalw : 2.1+lgpl-4 >>>> ea-utils : 1.1.2+dfsg-1biolinux1 >>>> emperor : 0.9.51-0biolinux1 >>>> fasttree : 2.1.7-1biolinux1.1 >>>> infernal : 1.1.1-2ubuntu1 >>>> mafft : 7.215-0biolinux1 >>>> mothur : 1.34.4+repack-0biolinux1 >>>> muscle : 1:3.8.31-1 >>>> parsinsert : 1.04-1biolinux1.1 >>>> pynast : 1.2.2-0biolinux1.1 >>>> python : 2.7.5-5ubuntu3 >>>> python-biom-format : 2.1.4-0biolinux2 >>>> python-burrito : 0.9.0-0biolinux3 >>>> python-burrito-fillings : 0.1.0-0biolinux4 >>>> python-cogent : 1.5.3-2biolinux2 >>>> python-matplotlib : 1.3.1-1ubuntu5 >>>> python-mpi4py : 1.3.1+hg20131106-1build3 >>>> python-numpy : 1:1.8.2-0ubuntu0.1 >>>> python-pandas : 0.13.1-2ubuntu2 >>>> python-qcli : 0.1.0-1 >>>> python : 2.7.5-5ubuntu3 >>>> qiime-data : 1.9.0+dfsg-0biolinux5 >>>> qiime-default-reference : 0.1.1-0biolinux2 >>>> r-cran-optparse : 1.3.0-1cran1ppa0 >>>> raxml : 8.0.26-0biolinux1 >>>> rdp-classifier : 2.10.2+dfsg-0biolinux1 >>>> seqprep : 1.1-0biolinux2 >>>> sortmerna : 2.0-0biolinux1 >>>> sumatra : 1.0.01-0ubuntu1 >>>> swarm : 1.2.20-0biolinux1 >>>> vsearch : 1.1.1.nodata-0biolinux1 >>>> >>>> OK >>>> >>>> -- Dipl. Biol. Marvin Djukic Georg-August Universit?t G?ttingen Institut f?r Mikrobiologie und Genetik G?ttingen Genomics Laboratory Grisebachstra?e 8 37077 G?ttingen Germany Tel. 0049-(0)551-39-33843 Mobil: 0176-45743636 E-Mail: mdjukic1 at gwdg.de http://appmibio.uni-goettingen.de From tbooth at ceh.ac.uk Fri Jul 31 09:01:49 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 31 Jul 2015 14:01:49 +0100 Subject: [Bio-Linux] qiime filter_fasta.py problem In-Reply-To: <55BB695E.2040208@gwdg.de> References: <55BB2E85.8040505@gwdg.de> <1438340555.5557.396.camel@wllt1771.nerc-wallingford.ac.uk> <55BB5E60.8090209@gwdg.de> <1438345296.5557.404.camel@wllt1771.nerc-wallingford.ac.uk> <55BB695E.2040208@gwdg.de> Message-ID: <1438347709.5557.428.camel@wllt1771.nerc-wallingford.ac.uk> No worries. Glad to be of help. TIM On Fri, 2015-07-31 at 14:26 +0200, Marvin Djukic wrote: > Hi Tim, > > You're right - I guess I manually installed it the wrong way and didn't > delete all "old" files. > And yes, that fixed it. MANY many thanks. > > Regards, > Marvin >