From tbooth at ceh.ac.uk Fri Mar 25 05:38:09 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 25 Mar 2011 09:38:09 +0000 Subject: [Bio-linux-dev] Qiime 1.2.1 Message-ID: <1301045889.3382.17218.camel@barsukas> Hi All, As promised, I'm currently working on the Qiime repackaging for 1.2.1. The Qiime package itself is rather small but has many dependencies and there are what cause all the aggro. I know there are further updates needed but in the meantime, I've started by re-rolling the Qiime package. If you are able to try this in the next couple of days and let me know what does/doesn't work I'll try to fix things as fast as I can. I'm also doing my own testing here and hopefully by early next week I'll have all the results in the package repository for a one-click install. As the package currently is half-baked, the instructions to install are a bit longer than the usual 'apt-get install bio-linux-qiime'... Instructions: 1) sudo apt-get remove bio-linux-qiime # This will report that you do not need various packages any more - # ignore this - you DO still need them. 2) wget http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb wget http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb 3) sudo dpkg -i qiime_1.2.1-ubuntu4_all.deb sudo dpkg -i python-cogent_1.5-2_amd64.deb 4) Grab uclustq1.2.21_i86linux64 from http://www.drive5.com/uclust/downloads1_2_21q.html sudo cp uclustq1.2.21_i86linux64 /usr/local/bin/uclust sudo chmod a+rx /usr/local/bin/uclust 5) As before, type 'qiime' to get into the qiime shell. Alternatively you can now also invoke a single Qiime command like so: qiime check_id_map [...] Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From mikeyj.cox at gmail.com Fri Mar 25 06:27:31 2011 From: mikeyj.cox at gmail.com (Mike Cox) Date: Fri, 25 Mar 2011 10:27:31 +0000 Subject: [Bio-linux-dev] Qiime 1.2.1 In-Reply-To: <1301045889.3382.17218.camel@barsukas> References: <1301045889.3382.17218.camel@barsukas> Message-ID: Tim, We love you. I'll try this out as soon as possible and get back to you with any problems. Thanks Mike Mike Cox Research Associate Centre for Respiratory Infection National Heart Lung Institute Royal Brompton Campus Guy Scadding Building London SW3 6LY michael.cox1 at imperial.ac.uk http://www1.imperial.ac.uk/medicine/people/michael.cox1/ On Fri, Mar 25, 2011 at 09:38, Tim Booth wrote: > Hi All, > > As promised, I'm currently working on the Qiime repackaging for 1.2.1. > The Qiime package itself is rather small but has many dependencies and > there are what cause all the aggro. I know there are further updates > needed but > in the meantime, I've started by re-rolling the Qiime package. > > If you are able to try this in the next couple of days and let me know > what does/doesn't work I'll try to fix things as fast as I can. I'm > also doing my own testing here and hopefully by early next week I'll > have all the results in the package repository for a one-click install. > > As the package currently is half-baked, the instructions to install are > a bit longer than the usual 'apt-get install bio-linux-qiime'... > > Instructions: > > 1) > sudo apt-get remove bio-linux-qiime > > # This will report that you do not need various packages any more - > # ignore this - you DO still need them. > > 2) > wget > http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb > wget > http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb > > 3) > sudo dpkg -i qiime_1.2.1-ubuntu4_all.deb > sudo dpkg -i python-cogent_1.5-2_amd64.deb > > 4) > Grab uclustq1.2.21_i86linux64 from > http://www.drive5.com/uclust/downloads1_2_21q.html > > sudo cp uclustq1.2.21_i86linux64 /usr/local/bin/uclust > sudo chmod a+rx /usr/local/bin/uclust > > 5) > As before, type 'qiime' to get into the qiime shell. Alternatively you can > now also > invoke a single Qiime command like so: > > qiime check_id_map [...] > > Cheers, > > TIM > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.l.ostrowski at gmail.com Sun Mar 27 16:25:01 2011 From: m.l.ostrowski at gmail.com (Martin Ostrowski) Date: Sun, 27 Mar 2011 21:25:01 +0100 Subject: [Bio-linux-dev] Qiime 1.2.1 In-Reply-To: <1301045889.3382.17218.camel@barsukas> References: <1301045889.3382.17218.camel@barsukas> Message-ID: <4A38F21A-E861-4507-9301-8315AFAE7F4F@gmail.com> Hi Tim, I think that I missed the window to download the qiime and pycogent packages. The server with those packages is not responding. Thanks for your help with this package. After many headaches I got a partial build of Qiime 1.2.1 and dependencies going on my Mac server but there are a few Warwick people now asking me about additional functions. We should be able to give it a good test this week. Thanks again Martin On 25 Mar 2011, at 09:38, Tim Booth wrote: > Hi All, > > As promised, I'm currently working on the Qiime repackaging for 1.2.1. > The Qiime package itself is rather small but has many dependencies and > there are what cause all the aggro. I know there are further updates needed but > in the meantime, I've started by re-rolling the Qiime package. > > If you are able to try this in the next couple of days and let me know > what does/doesn't work I'll try to fix things as fast as I can. I'm > also doing my own testing here and hopefully by early next week I'll > have all the results in the package repository for a one-click install. > > As the package currently is half-baked, the instructions to install are > a bit longer than the usual 'apt-get install bio-linux-qiime'... > > Instructions: > > 1) > sudo apt-get remove bio-linux-qiime > > # This will report that you do not need various packages any more - > # ignore this - you DO still need them. > > 2) > wget http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb > wget http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb > > 3) > sudo dpkg -i qiime_1.2.1-ubuntu4_all.deb > sudo dpkg -i python-cogent_1.5-2_amd64.deb > > 4) > Grab uclustq1.2.21_i86linux64 from http://www.drive5.com/uclust/downloads1_2_21q.html > > sudo cp uclustq1.2.21_i86linux64 /usr/local/bin/uclust > sudo chmod a+rx /usr/local/bin/uclust > > 5) > As before, type 'qiime' to get into the qiime shell. Alternatively you can now also > invoke a single Qiime command like so: > > qiime check_id_map [...] > > Cheers, > > TIM > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev From tbooth at ceh.ac.uk Mon Mar 28 05:49:08 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 28 Mar 2011 10:49:08 +0100 Subject: [Bio-linux-dev] CEH network and servers Message-ID: <1301305748.1947.129.camel@barsukas> Hi All, Apologies to Martin and anyone else who tried to download Qiime over the weekend. Due to maintenance in the server room we lost network access and so the web server was unreachable. The mailing list server was also offline so this mailing list was also out of action. There is more maintenance work scheduled for next weekend, but in the meantime everything should be back and accessible. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.