From tauqeer9 at gmail.com Fri Oct 4 21:14:46 2013 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Fri, 4 Oct 2013 21:14:46 -0400 Subject: [Bio-Linux] External hard drive for Biolinux Message-ID: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> Hi All I am planning to purchase an external hard drive for data back up, but do not which drive works better for Biolinux. I have heard that external drives are OS specific, so wanted to be sure before I purchase it. I see Mac and Window compatible drives on amazon but none of them talk about Linux. Does Western Digital My Passport 2TB work for Biolinux? Any suggestion will be appreciated. Thanks Tauqeer From tony.travis at abdn.ac.uk Sat Oct 5 05:56:03 2013 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 5 Oct 2013 10:56:03 +0100 Subject: [Bio-Linux] External hard drive for Biolinux In-Reply-To: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> References: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> Message-ID: <524FE233.9090705@abdn.ac.uk> On 05/10/13 02:14, Tauqeer Alam wrote: > Hi All I am planning to purchase an external hard drive for data back > up, but do not which drive works better for Biolinux. I have heard > that external drives are OS specific, so wanted to be sure before I > purchase it. I see Mac and Window compatible drives on amazon but > none of them talk about Linux. Does Western Digital My Passport 2TB > work for Biolinux? Any suggestion will be appreciated. Hi, Tauqeer. The external drives are only OS-specific in that some are pre-formatted for Mac or Windows and have a partition on them with proprietary backup software. We've used 'Mac' 2TB WD My-MyBook's for backup: Just repartition with an MSDOS disk label and reformat them to Linux ext4. If you want to use my ETOH backup, you need to run Tim's setup script. HTH, 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. From kissaj at miamioh.edu Sun Oct 6 08:53:15 2013 From: kissaj at miamioh.edu (Andor J Kiss) Date: Sun, 06 Oct 2013 08:53:15 -0400 Subject: [Bio-Linux] External hard drive for Biolinux In-Reply-To: <524FE233.9090705@abdn.ac.uk> References: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> <524FE233.9090705@abdn.ac.uk> Message-ID: <1381063995.6875.148.camel@methy1> Hi, I've actually heard that some Seagate Drives have firmware that only works with Windows. We use LaCie backup drives that come with a linux based (GUI) management system to backup our BioLinux workstations: http://www.lacie.com/us/products/product.htm?id=10584 Regards, Andor On Sat, 2013-10-05 at 10:56 +0100, Tony Travis wrote: > On 05/10/13 02:14, Tauqeer Alam wrote: > > Hi All I am planning to purchase an external hard drive for data back > > up, but do not which drive works better for Biolinux. I have heard > > that external drives are OS specific, so wanted to be sure before I > > purchase it. I see Mac and Window compatible drives on amazon but > > none of them talk about Linux. Does Western Digital My Passport 2TB > > work for Biolinux? Any suggestion will be appreciated. > > Hi, Tauqeer. > > The external drives are only OS-specific in that some are pre-formatted > for Mac or Windows and have a partition on them with proprietary backup > software. We've used 'Mac' 2TB WD My-MyBook's for backup: Just > repartition with an MSDOS disk label and reformat them to Linux ext4. > > If you want to use my ETOH backup, you need to run Tim's setup script. > > HTH, > > 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. > _______________________________________________ > 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 tony.travis at abdn.ac.uk Sun Oct 6 18:16:54 2013 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sun, 6 Oct 2013 23:16:54 +0100 Subject: [Bio-Linux] External hard drive for Biolinux In-Reply-To: <1381063995.6875.148.camel@methy1> References: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> <524FE233.9090705@abdn.ac.uk> <1381063995.6875.148.camel@methy1> Message-ID: <5251E156.10707@abdn.ac.uk> On 06/10/13 13:53, Andor J Kiss wrote: > Hi, > > I've actually heard that some Seagate Drives have firmware that only > works with Windows. We use LaCie backup drives that come with a linux > based (GUI) management system to backup our BioLinux workstations: > http://www.lacie.com/us/products/product.htm?id=10584 Hi, Andor. Hmm... I only know about Apple using custom firmware. However, these 'Apple' disks worked fine under Linux ;-) I'd be interested to know more? 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. From tauqeer9 at gmail.com Sun Oct 6 19:03:06 2013 From: tauqeer9 at gmail.com (Tauqeer Alam) Date: Sun, 6 Oct 2013 19:03:06 -0400 Subject: [Bio-Linux] External hard drive for Biolinux In-Reply-To: <5251E156.10707@abdn.ac.uk> References: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> <524FE233.9090705@abdn.ac.uk> <1381063995.6875.148.camel@methy1> <5251E156.10707@abdn.ac.uk> Message-ID: Thank you all for your suggestions. This is very helpful. Tauqeer On Sun, Oct 6, 2013 at 6:16 PM, Tony Travis wrote: > On 06/10/13 13:53, Andor J Kiss wrote: > > Hi, > > > > I've actually heard that some Seagate Drives have firmware that only > > works with Windows. We use LaCie backup drives that come with a linux > > based (GUI) management system to backup our BioLinux workstations: > > http://www.lacie.com/us/products/product.htm?id=10584 > > Hi, Andor. > > Hmm... I only know about Apple using custom firmware. > > However, these 'Apple' disks worked fine under Linux ;-) > > I'd be interested to know more? > > 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. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- ********************************************* Md Tauqeer Alam, Ph.D Division of Infectious Diseases Emory University School of Medicine 615 Michael Street, Atlanta, GA 30322, USA tauqeer9 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From joasch at MBA.ac.uk Tue Oct 8 10:28:35 2013 From: joasch at MBA.ac.uk (Joanna Schroeder) Date: Tue, 8 Oct 2013 15:28:35 +0100 Subject: [Bio-Linux] cdhit in qiime Message-ID: Hello Tim and/or the Biolinux team, I'm struggling to get the cdhit otu picking method working within Qiime. I wondered if you had any suggestions or recommendations of how to proceed with this. e.g I use the command pick_otus.py -i /home/joasch/Rarefaction/Data/Pro/BacCombined.fa -m cdhit -t -M 2000 -o /home/joasch/Rarefaction/Data/Pro/OpenOTU and the error I get is Traceback (most recent call last): File "/usr/lib/qiime/bin/pick_otus.py", line 771, in main() File "/usr/lib/qiime/bin/pick_otus.py", line 579, in main trie_prefilter=trie_prefilter) File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", line 697, in __call__ seqs=seqs,moltype=moltype,params=cd_hit_params) File "/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py", line 260, in cdhit_clusters_from_seqs remove(params['-o'] + '.bak.clstr') OSError: [Errno 2] No such file or directory: '/tmp/tmpwmVbfmpFIo2z0DnhDWhm.txt.bak.clstr' I'm not quite sure how to interpret or get round this. I'd really appreciate any recommendations, Thanks and best regards, Jo Dr Jo Schroeder Research Assistant (Bioinformatics and Statistics) The Marine Biological Association of the UK, Plymouth joasch at mba.ac.uk From daniel.antony.pass at googlemail.com Tue Oct 8 11:15:08 2013 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Tue, 8 Oct 2013 16:15:08 +0100 Subject: [Bio-Linux] cdhit in qiime In-Reply-To: References: Message-ID: I don't know for certain, but I'm wondering if having such a high ram allocation could be knocking it over. Is this server based as 2gb could be pushing it for an oldish desktop? Also, I've known on occasion that if you've got multiple cores specified in a parameters file qiime would run it parallel even if not specified specifically in the command and this would duplicate the ram. If you turn the -M down or to default does that stop the error? Also, the qiime forum is pretty quick to help with things like this: https://groups.google.com/forum/#!forum/qiime-forum Dan On 8 October 2013 15:28, Joanna Schroeder wrote: > Hello Tim and/or the Biolinux team, > > I'm struggling to get the cdhit otu picking method working within Qiime. > I wondered if you had any suggestions or recommendations of how to proceed > with this. e.g I use the command > > pick_otus.py -i /home/joasch/Rarefaction/Data/Pro/BacCombined.fa -m cdhit > -t -M 2000 -o /home/joasch/Rarefaction/Data/Pro/OpenOTU > > and the error I get is > > Traceback (most recent call last): > File "/usr/lib/qiime/bin/pick_otus.py", line 771, in > main() > File "/usr/lib/qiime/bin/pick_otus.py", line 579, in main > trie_prefilter=trie_prefilter) > File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", line 697, in > __call__ > seqs=seqs,moltype=moltype,params=cd_hit_params) > File "/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py", line 260, > in cdhit_clusters_from_seqs > remove(params['-o'] + '.bak.clstr') > OSError: [Errno 2] No such file or directory: > '/tmp/tmpwmVbfmpFIo2z0DnhDWhm.txt.bak.clstr' > > I'm not quite sure how to interpret or get round this. I'd really > appreciate any recommendations, > > Thanks and best regards, > Jo > > > Dr Jo Schroeder > Research Assistant (Bioinformatics and Statistics) > The Marine Biological Association of the UK, Plymouth > joasch at mba.ac.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- Daniel Pass Tel: (029208)76680 Mob: 07735658687 http://www.kille-morgan.org.uk Room 0.39, School of Biosciences, Biological Sciences Building, Museum Avenue, Cardiff, CF10 3AT -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Oct 8 11:43:53 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 8 Oct 2013 16:43:53 +0100 Subject: [Bio-Linux] cdhit in qiime In-Reply-To: References: Message-ID: <1381247033.3844.492.camel@balisaur> Hi, I think the problem is more mundane. CD-HIT always used to leave behind a certain temporary file, and so QIIME (or rather the Cogent library it uses) manually cleans it up after each run. A recent update to CD-HIT removes this bug and the file is now cleaned up within CD-HIT. But when QIIME tries to remove the file and can't find it, it craps out. What it should do it just press on regardless. I'm applying and testing a simple patch just now. Will push it as an update if it works. Cheers, TIM On Tue, 2013-10-08 at 16:15 +0100, Daniel Pass wrote: > I don't know for certain, but I'm wondering if having such a high ram > allocation could be knocking it over. Is this server based as 2gb > could be pushing it for an oldish desktop? Also, I've known on > occasion that if you've got multiple cores specified in a parameters > file qiime would run it parallel even if not specified specifically in > the command and this would duplicate the ram. > > > If you turn the -M down or to default does that stop the error? > > > Also, the qiime forum is pretty quick to help with things like > this: https://groups.google.com/forum/#!forum/qiime-forum > > > Dan > > > On 8 October 2013 15:28, Joanna Schroeder wrote: > Hello Tim and/or the Biolinux team, > > I'm struggling to get the cdhit otu picking method working > within Qiime. I wondered if you had any suggestions or > recommendations of how to proceed with this. e.g I use the > command > > pick_otus.py > -i /home/joasch/Rarefaction/Data/Pro/BacCombined.fa -m cdhit > -t -M 2000 -o /home/joasch/Rarefaction/Data/Pro/OpenOTU > > and the error I get is > > Traceback (most recent call last): > File "/usr/lib/qiime/bin/pick_otus.py", line 771, in > > main() > File "/usr/lib/qiime/bin/pick_otus.py", line 579, in main > trie_prefilter=trie_prefilter) > File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", > line 697, in __call__ > seqs=seqs,moltype=moltype,params=cd_hit_params) > File > "/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py", line > 260, in cdhit_clusters_from_seqs > remove(params['-o'] + '.bak.clstr') > OSError: [Errno 2] No such file or directory: > '/tmp/tmpwmVbfmpFIo2z0DnhDWhm.txt.bak.clstr' > > I'm not quite sure how to interpret or get round this. I'd > really appreciate any recommendations, > > Thanks and best regards, > Jo > > > Dr Jo Schroeder > Research Assistant (Bioinformatics and Statistics) > The Marine Biological Association of the UK, Plymouth > joasch at mba.ac.uk > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > -- > > > > Daniel Pass > > Tel: (029208)76680 > Mob: 07735658687 > http://www.kille-morgan.org.uk > > Room 0.39, > School of Biosciences, > Biological Sciences Building, > Museum Avenue, > Cardiff, > CF10 3AT > -- 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 From tony.travis at abdn.ac.uk Wed Oct 16 11:30:17 2013 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 16 Oct 2013 16:30:17 +0100 Subject: [Bio-Linux] problem running picard-tools under Bio-Linux Message-ID: <525EB109.20200@abdn.ac.uk> Hi, We've had problems running picard-tools under Bio-Linux 7 because the CLASSPATH was not set, and the wrapper script does not set -cp for the sam and bzip2 jars. It works if I set the java -cp paths explicity in the wrapper: HTH, Tony. > rwt017 at wildcat:~$ diff -Naur /usr/bin/picard-tools /usr/local/bin/test-picard-tools > --- /usr/bin/picard-tools 2013-08-16 14:45:04.000000000 +0100 > +++ /usr/local/bin/test-picard-tools 2013-10-16 14:44:44.347312505 +0100 > @@ -1,6 +1,6 @@ > #!/bin/sh > set -eu > -if [ `basename -- $0` = picard-tools ]; then > +if [ `basename -- $0` = test-picard-tools ]; then > if [ $# = 0 ]; then > cat 1>&2 < picard-tools: missing command argument > @@ -56,4 +56,4 @@ > > # Note, jbzip2.jar and sam.jar etc. should now be added to cp implicitly > p=/usr/share/java > -exec java -XX:MaxPermSize=256m -cp $p/picard.jar $main "$@" > +exec java -XX:MaxPermSize=256m -cp $p/picard.jar:sam.jar:$p/jbzip2.jar $main "$@" -- 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. From kissaj at miamioh.edu Wed Oct 16 13:50:56 2013 From: kissaj at miamioh.edu (Andor J Kiss) Date: Wed, 16 Oct 2013 13:50:56 -0400 Subject: [Bio-Linux] External hard drive for Biolinux In-Reply-To: <5251E156.10707@abdn.ac.uk> References: <74D306A9-2CB0-4E49-A614-A1EBB7A721E8@gmail.com> <524FE233.9090705@abdn.ac.uk> <1381063995.6875.148.camel@methy1> <5251E156.10707@abdn.ac.uk> Message-ID: <1381945856.4997.11.camel@methy1> Maybe this was only with older versions of Ubuntu - that what came up on google - looks as if 12.04 is pretty good with USB drives -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and 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://www.cas.muohio.edu/cbfg URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss On Sun, 2013-10-06 at 23:16 +0100, Tony Travis wrote: > On 06/10/13 13:53, Andor J Kiss wrote: > > Hi, > > > > I've actually heard that some Seagate Drives have firmware that only > > works with Windows. We use LaCie backup drives that come with a linux > > based (GUI) management system to backup our BioLinux workstations: > > http://www.lacie.com/us/products/product.htm?id=10584 > > Hi, Andor. > > Hmm... I only know about Apple using custom firmware. > > However, these 'Apple' disks worked fine under Linux ;-) > > I'd be interested to know more? > > 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. > _______________________________________________ > 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: