From maxime.gommeaux at univ-reims.fr Tue Jan 31 04:32:33 2017 From: maxime.gommeaux at univ-reims.fr (Maxime GOMMEAUX) Date: Tue, 31 Jan 2017 10:32:33 +0100 Subject: [Bio-linux-list] How to update mothur? Message-ID: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> Dear users of Bio-Linux, I have been an enthusiastic user of the Bio-Linux distribution for ~2years and I appreciate it greatly. I would like, however, to update the mothur package to try their new clustering algorithm, included in the brand-new release 1.39. If I remember well, originally the version of mothur was 1.34 at the time I installed the distro. Some time later it upgraded to 1.36 "automatically" (with the normal system updates), but it has been stuck since then. Thus, I would like to update mothur "manually", but I don't want to wreck my system. Remark: the Ubuntu base is still 14.04 (I have refused the 16.04 upgrade to date, but maybe I should do this first???). Thank you for any help! Maxime -- Maxime GOMMEAUX, ma?tre de conf?rences - Affiliation: Universit? de Reims Champagne-Ardenne, UFR Sciences, D?partement des sciences de la Terre Laboratoire GEGENAA, EA 3795 - Adresse de visite ou postale: CREA, 2 esplanade Roland Garros F-51100 Reims (GPS: 49.2385?N; 4.0625?E) - T?l: +33 3 26 77 36 83 - http://www.univ-reims.fr http://www.univ-reims.fr/gegenaa Avec l'URCA, soutenez la candidature de la France ? l'exposition universelle de 2025! From tony.travis at minke-informatics.co.uk Tue Jan 31 07:13:08 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 31 Jan 2017 12:13:08 +0000 Subject: [Bio-linux-list] How to update mothur? In-Reply-To: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> References: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> Message-ID: On 31/01/17 09:32, Maxime GOMMEAUX wrote: > Dear users of Bio-Linux, > > I have been an enthusiastic user of the Bio-Linux distribution for > ~2years and I appreciate it greatly. Hi, Maxime. I'm glad you like Bio-Linux :-) > I would like, however, to update the mothur package to try their new > clustering algorithm, included in the brand-new release 1.39. OK, but this version is NOT yet packaged for Debian/Ubuntu and, as you probably already know, you have to get it from GitHub: > https://github.com/mothur/mothur/releases/tag/v1.39.0 [The repository also contains updated binaries of supporting programs] > If I remember well, originally the version of mothur was 1.34 at the > time I installed the distro. Some time later it upgraded to 1.36 > "automatically" (with the normal system updates), but it has been stuck > since then. You're right that the current version is 1.36: > root at wildcat:~# apt-cache policy mothur > mothur: > Installed: 1.36.1+dfsg-0biolinux1 > Candidate: 1.36.1+dfsg-0biolinux1 > Version table: > *** 1.36.1+dfsg-0biolinux1 0 > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages > 100 /var/lib/dpkg/status > 1.31.2+dfsg-2build1 0 > 500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages > 1.22.2-2 0 > 500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages > root at wildcat:~# This is because Tim Booth, the lead developer, has now left the project and I am seeking funding to continue it. However, I'm just answering any queries on the Bio-Linux list at present not updating packages. > Thus, I would like to update mothur "manually", but I don't want to > wreck my system. Remark: the Ubuntu base is still 14.04 (I have refused > the 16.04 upgrade to date, but maybe I should do this first???). I've upgraded several Bio-linux 8 Ubuntu 14.04 LTS instances to 16.04 LTS, but many packages break and I don't recommend doing that unless you are prepared to enter 'package-dependency-hell' :-( Even if you did, you would get the same version of "mothur". This is on my Bio-Linux 8 laptop "beluga", which I've upgraded to Ubuntu 16.04 LTS: > ajt at beluga:~$ lsb_release -d > Description: Ubuntu 16.04.1 LTS > ajt at beluga:~$ apt-cache policy mothur > mothur: > Installed: (none) > Candidate: 1.36.1+dfsg-0biolinux1 > Version table: > 1.36.1+dfsg-0biolinux1 500 > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64 Packages > 1.36.1-1build1 500 > 500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages I've not installed "mothur" because of the 'package-dependency-hell'... If you want to try updating "mothur" manually under Bio-Linux 8 (Ubuntu 14.04), download the binaaries from GitHub: > wget https://github.com/mothur/mothur/releases/download/v1.39.0/Mothur.linux_64.zip Then extract it and install just the "mothur" binary: > unzip Mothur.linux_64.zip > ls -R mothur > mothur: > blast CatchAllCmdL.exe LICENSE mothur uchime vsearch > > mothur/blast: > bin > > mothur/blast/bin: > bl2seq blastall blastclust blastpgp copymat fastacmd formatdb formatrpsdb impala makemat megablast rpsblast seedtop > cp -ai mothur/mothur /usr/local/bin/ This will place the updated version of "mothur" ahead of the previously installed version on your PATH: > which -a mothur > /usr/local/bin/mothur > /usr/bin/mothur Try running this version, but you may need to copy other supporting binaries from the .zip file into /usr/local/bin. However, that may well break other things in Bio-Linux, especially QIIME... > Thank you for any help! OK, let me know how you get on? Thanks, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From kissaj at miamioh.edu Tue Jan 31 07:20:26 2017 From: kissaj at miamioh.edu (Andor J Kiss) Date: Tue, 31 Jan 2017 07:20:26 -0500 Subject: [Bio-linux-list] How to update mothur? In-Reply-To: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> References: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> Message-ID: <1485865226.4928.11.camel@miamioh.edu> You can simply download latest mothur and unzip the file. ?Then navigate to the folder that the unzipped folder is in and start mothur $ /path/to/unzipped/mothur/folder/ ./mothur -- _________________________________________________________________________________________________________________________ Andor J Kiss, PhD Director - Center for Bioinformatics & Functional Genomics 086 Pearson Hall - Miami University 700 East High Street, Oxford, Ohio 45056 USA eMAIL: KissAJ at MiamiOH.edu? Telephone: +1-513-529-4280 Fax: +1-513-529-2431 URL (CBFG):?http://miamioh.edu/cas/academics/centers/cbfg/? URL (CBFG Services):?https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics URL (Research):?http://openwetware.org/wiki/User:Andor_J_Kiss? On Tue, 2017-01-31 at 10:32 +0100, Maxime GOMMEAUX wrote: > Dear users of Bio-Linux, > > I have been an enthusiastic user of the Bio-Linux distribution for? > ~2years and I appreciate it greatly. > > I would like, however, to update the mothur package to try their new? > clustering algorithm, included in the brand-new release 1.39. > > If I remember well, originally the version of mothur was 1.34 at the? > time I installed the distro. Some time later it upgraded to 1.36? > "automatically" (with the normal system updates), but it has been > stuck? > since then. > > Thus, I would like to update mothur "manually", but I don't want to? > wreck my system. Remark: the Ubuntu base is still 14.04 (I have > refused? > the 16.04 upgrade to date, but maybe I should do this first???). > > Thank you for any help! > > Maxime > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Tue Jan 31 08:07:29 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 31 Jan 2017 13:07:29 +0000 Subject: [Bio-linux-list] How to update mothur? In-Reply-To: <1485865226.4928.11.camel@miamioh.edu> References: <27768b4b-3562-c676-4863-4e608e14c9b4@univ-reims.fr> <1485865226.4928.11.camel@miamioh.edu> Message-ID: On 31/01/17 12:20, Andor J Kiss wrote: > You can simply download latest mothur and unzip the file. Then > navigate to the folder that the unzipped folder is in and start > mothur > > $ /path/to/unzipped/mothur/folder/ ./mothur -- Hi, Andor. You're right, that would probably be OK for testing, but not for 'normal' use - That's why I suggested copying the "mothur" binary to /usr/local/bin/ so it will be accessible via the shell PATH variable. However, none of the supporting programs in the .zip file will be accessible if you just run "./mothur" unless you add "." and "./blast/bin" to the PATH, but putting "." on the PATH is a potential security risk because of 'malware' and I do NOT advise doing it, even for testing... It's also 'bad-practice' to put executables and data in the same folder, but I only do it when there is no alternative :-) Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk