From mictadlo at gmail.com Tue Aug 4 02:57:08 2015 From: mictadlo at gmail.com (Mic) Date: Tue, 4 Aug 2015 16:57:08 +1000 Subject: [Bio-Linux] IPython Notebook integration in Galaxy Message-ID: Hello, Does Bio-Linux has IPython Notebook integration in Galaxy like shown here ( https://www.youtube.com/watch?v=jQDyTuYnn1k ) or here ( https://github.com/bgruening/galaxy-ipython )? Is the Bio-Linux Galaxy version the same as on usegalaxy.org? Thank you in advance. Mic -------------- next part -------------- An HTML attachment was scrubbed... URL: From mictadlo at gmail.com Tue Aug 4 03:02:31 2015 From: mictadlo at gmail.com (Mic) Date: Tue, 4 Aug 2015 17:02:31 +1000 Subject: [Bio-Linux] Have Galaxy in Bio-Linux and usegalaxy.org the same tool installed Message-ID: Hello, Have Galaxy in Bio-Linux and usegalaxy.org the same tool installed? 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-LinuxGalaxy. Thank you in advance. Mic -------------- next part -------------- An HTML attachment was scrubbed... URL: From mark.fernandes at ifr.ac.uk Tue Aug 4 07:09:51 2015 From: mark.fernandes at ifr.ac.uk (mark fernandes (IFR)) Date: Tue, 4 Aug 2015 11:09:51 +0000 Subject: [Bio-Linux] IPython Notebook integration in Galaxy Message-ID: <8254360FC3FACF4B86D767D5D10A835B01436C01F7@MAILEX2.nbi.ac.uk> The Ipython integration is part of "Interactive Environments" for Galaxy and uses Docker to serve Ipython requests and integrate galaxy outputs & inputs through Python. So unless Biolinux includes Docker... Bjorn & Eric gave an excellent presentation on their work on Integrative Environments at the Galaxy Community Conference this year (http://gcc2015.tsl.ac.uk/abstracts/#Galaxy_Interactive_Environments_8211_a_new_way_to_interact_with_your_data ) You could always create a linux VM in VirtualBox and then install Docker and then pull the docker images from Bjorn's Github to run Galaxy with Int.Env.. Hope that this helps, Mark Fernandes Bioinformatics/Biomathematics Training T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC From mark.fernandes at ifr.ac.uk Tue Aug 4 12:02:52 2015 From: mark.fernandes at ifr.ac.uk (mark fernandes (IFR)) Date: Tue, 4 Aug 2015 16:02:52 +0000 Subject: [Bio-Linux] Have Galaxy in Bio-Linux and usegalaxy.org the same tool installed Message-ID: <8254360FC3FACF4B86D767D5D10A835B01436C028B@MAILEX2.nbi.ac.uk> You may also be able to use that xml list of the URLs to the tools to install them using a Dockerfile like this: ----------------------------------------------------------- FROM bgruening/galaxy-stable:15.05 MAINTAINER Bj?rn A. Gr?ning, bjoern.gruening at gmail.com ENV GALAXY_CONFIG_BRAND GalaxyFlavorGenerator WORKDIR /galaxy-central RUN install-repository \ "--url https://testtoolshed.g2.bx.psu.edu/ -o hackdna --name FastQC checker" \ "--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name Manipulate FASTQ" \ "--url https://testtoolshed.g2.bx.psu.edu/ -o nilesh --name RNASeQC" \ "--url https://testtoolshed.g2.bx.psu.edu/ -o jjohnson --name Trinity read normalization" \ "--url https://testtoolshed.g2.bx.psu.edu/ -o jjohnson --name Trinity" \ "--url https://testtoolshed.g2.bx.psu.edu/ -o boris --name Filter mapped reads" \ VOLUME ["/export/", "/data/", "/var/lib/docker"] EXPOSE :80 EXPOSE :21 EXPOSE :8080 CMD ["/usr/bin/startup"] ------------------------------------------------------ NB Install-repository is a Galaxy script to install tools when building a Galaxy instance. Hope this helps you along, Mark Fernandes Bioinformatics/Biomathematics Training T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC From rjohns03 at carc.unm.edu Fri Aug 14 10:10:00 2015 From: rjohns03 at carc.unm.edu (Ryan Johnson) Date: Fri, 14 Aug 2015 08:10:00 -0600 Subject: [Bio-Linux] Fwd: Public Facing Galaxy Server Configuration In-Reply-To: <55C91641.7000109@carc.unm.edu> References: <55C91641.7000109@carc.unm.edu> Message-ID: <55CDF6B8.2010106@carc.unm.edu> Hi All, I have Bio-Linux + Galaxy set up to face the public on port 8080 (without Apache) for some quick proof of concept tests. But I am encountering an issue with users trying to access this machine from outside the local network. I have the Bio-Linux OS firewall temporarily disabled for debugging as well. My users on the local network can load the web interface but those on the WAN cannot. Are their more security settings I have to configure or is there a setting in the Galaxy-Server configuration file that I need to change? Kindly, Ryan -- Ryan S. Johnson, PhD Applications Scientist Center for Advanced Research Computing P: (650) 430-6194 E: rjohns03 at carc.unm.edu From tbooth at ceh.ac.uk Fri Aug 14 11:02:35 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 14 Aug 2015 16:02:35 +0100 Subject: [Bio-Linux] Fwd: Public Facing Galaxy Server Configuration In-Reply-To: <55CDF6B8.2010106@carc.unm.edu> References: <55C91641.7000109@carc.unm.edu> <55CDF6B8.2010106@carc.unm.edu> Message-ID: <1439564555.4466.155.camel@wllt1771.nerc-wallingford.ac.uk> Hi Ryan, I would imagine that your local network firewall is blocking incoming access on this port. The default settings on the Bio-Linux internal firewall do not try to distinguish between what is on the local network and what is on the wider internet, so if port 8080 is accessible from the computer next door it should be accessible from anywhere. You need to talk to your local network admins. They may say that opening port 8080 to the whole internet is insecure, and I'd be inclined to agree with them. You should consider if you can ask for specific trusted hosts to be given access. Failing that, if your machine is publicly accessible via SSH then you can tunnel the connection, so that people will only be able to see Galaxy once they have successfully connected with SSH. Let me know if you want more specifics on that. Cheers, TIM On Fri, 2015-08-14 at 08:10 -0600, Ryan Johnson wrote: > Hi All, > > I have Bio-Linux + Galaxy set up to face the public on port 8080 > (without Apache) for some quick proof of concept tests. But I am > encountering an issue with users trying to access this machine from > outside the local network. I have the Bio-Linux OS firewall temporarily > disabled for debugging as well. My users on the local network can load > the web interface but those on the WAN cannot. Are their more security > settings I have to configure or is there a setting in the Galaxy-Server > configuration file that I need to change? > > Kindly, > Ryan > > -- 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 tony.travis at minke-informatics.co.uk Fri Aug 14 11:56:50 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 14 Aug 2015 16:56:50 +0100 Subject: [Bio-Linux] Fwd: Public Facing Galaxy Server Configuration In-Reply-To: <55CDF6B8.2010106@carc.unm.edu> References: <55C91641.7000109@carc.unm.edu> <55CDF6B8.2010106@carc.unm.edu> Message-ID: <55CE0FC2.4080207@minke-informatics.co.uk> On 14/08/15 15:10, Ryan Johnson wrote: > Hi All, > > I have Bio-Linux + Galaxy set up to face the public on port 8080 > (without Apache) for some quick proof of concept tests. But I am > encountering an issue with users trying to access this machine from > outside the local network. I have the Bio-Linux OS firewall temporarily > disabled for debugging as well. My users on the local network can load > the web interface but those on the WAN cannot. Are their more security > settings I have to configure or is there a setting in the Galaxy-Server > configuration file that I need to change? Hi, Ryan. You can run Galaxy on port 80 behind a proxy: http://wiki.galaxyproject.org/Admin/Config/Apache Proxy [I've done this where port 80 is open, but port 8080 is not] HTH, 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 tony.travis at minke-informatics.co.uk Fri Aug 14 12:18:40 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 14 Aug 2015 17:18:40 +0100 Subject: [Bio-Linux] Fwd: Public Facing Galaxy Server Configuration In-Reply-To: <55CE0FC2.4080207@minke-informatics.co.uk> References: <55C91641.7000109@carc.unm.edu> <55CDF6B8.2010106@carc.unm.edu> <55CE0FC2.4080207@minke-informatics.co.uk> Message-ID: <55CE14E0.1080100@minke-informatics.co.uk> On 14/08/15 16:56, Tony Travis wrote: > [...] > You can run Galaxy on port 80 behind a proxy: > > http://wiki.galaxyproject.org/Admin/Config/Apache Proxy Hi, Ryan. Try: "http://wiki.galaxyproject.org/Admin/Config/Apache Proxy" [Sorry, the URL was truncated by my TB because of the space] 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 From tbooth at ceh.ac.uk Mon Aug 17 04:47:11 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 17 Aug 2015 09:47:11 +0100 Subject: [Bio-Linux] Fwd: Public Facing Galaxy Server Configuration In-Reply-To: <55CE14E0.1080100@minke-informatics.co.uk> References: <55C91641.7000109@carc.unm.edu> <55CDF6B8.2010106@carc.unm.edu> <55CE0FC2.4080207@minke-informatics.co.uk> <55CE14E0.1080100@minke-informatics.co.uk> Message-ID: <1439801231.4466.164.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tony and Ryan, For the Apache proxy, you could try the manual set-up detailed there, or you could save yourself time and hassle by using the apache-proxy package detailed here: http://environmentalomics.org/bio-linux-galaxy/ Cheers, TIM On Fri, 2015-08-14 at 17:18 +0100, Tony Travis wrote: > On 14/08/15 16:56, Tony Travis wrote: > > [...] > > You can run Galaxy on port 80 behind a proxy: > > > > http://wiki.galaxyproject.org/Admin/Config/Apache Proxy > > Hi, Ryan. > > Try: "http://wiki.galaxyproject.org/Admin/Config/Apache Proxy" > > [Sorry, the URL was truncated by my TB because of the space] > > Bye, > > Tony. > -- 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 amanjain at imtech.res.in Tue Aug 18 10:24:43 2015 From: amanjain at imtech.res.in (amanjain at imtech.res.in) Date: Tue, 18 Aug 2015 07:24:43 -0700 Subject: [Bio-Linux] Fwd: Re:Help in running PanFunPro stand alone tool Message-ID: <6658197251b808879c4c07172acb73f1@imtech.res.in> Hi, I am having difficulty in running PanFunPro stand alone tool used to compare core and pan genes. I have installed all the required tools and after which I am running PanFunPro2profiles.pl file. No error is shown but "Queue: 1" starts printing and it does not end even after 1 day (snapshot attached). How should I go about it. Link to ARTICLE: http://f1000research.com/articles/2-265/v1 Links to the software : "https://zenodo.org/record/7583#.vcyaflokvc0" "http://www.cbs.dtu.dk/~oksana/phd_thesis/panfunpro/" Thankyou Best Regards, Aman Jain -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2015-08-04 19:43:54.png Type: image/png Size: 112421 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PanFunPro2profiles.pl Type: text/x-perl Size: 44071 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PanFunProScript_instructions.pdf Type: application/pdf Size: 20909 bytes Desc: not available URL: From tony.travis at minke-informatics.co.uk Tue Aug 18 10:51:41 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 18 Aug 2015 15:51:41 +0100 Subject: [Bio-Linux] Fwd: Re:Help in running PanFunPro stand alone tool In-Reply-To: <6658197251b808879c4c07172acb73f1@imtech.res.in> References: <6658197251b808879c4c07172acb73f1@imtech.res.in> Message-ID: <55D3467D.5060804@minke-informatics.co.uk> On 18/08/15 15:24, amanjain at imtech.res.in wrote: > Hi, > > I am having difficulty in running PanFunPro stand alone tool > used to compare core and pan genes. I have installed all the required > tools and after which I am running PanFunPro2profiles.pl file. No error > is shown but "Queue: 1" starts printing and it does not end even after 1 > day (snapshot attached). How should I go about it. > > Link to ARTICLE: http://f1000research.com/articles/2-265/v1 > > Links to the software : "https://zenodo.org/record/7583#.vcyaflokvc0" > "http://www.cbs.dtu.dk/~oksana/phd_thesis/panfunpro/" Hi, Aman. It looks like "PanFunPro2profiles.pl" is stuck in this loop because "InterProScan" is not creating the output file that it's looking for: > for (my $i=0;$i<=$#CF || @queue > 0;) { > if (@queue < $num2scan && $i <= $#CF) { > my $file_in = $CF[$i]; > system "cp $file_in $interpro_path"; > system "$interpro_path/interproscan.sh -ms 1 -f TSV --iprlookup --goterms --pathways -appl PfamA,TIGRFAM,SuperFamily -i $file_in -b $file_in.Interpro"; > push (@queue, $file_in); > sleep 10; > $i++; > next; > } > print "Queue: ". at queue."\n"; > for (my $j=0;$j<=$#queue;) { > my $filename = $interpro_path."/".$queue[$j].".Interpro.tsv"; > if (-e $filename) { ^^^^^^^^^^^^^^^^^ > splice (@queue, $j, 1); > last; ^^^^^ > } > $j++; > } > sleep 10; > I would check that your "InterProScan" installation is working properly before debugging the script. However, you can use the Perl debugger: perl -d PanFunPro2profiles.pl ... HTH, 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 amanjain at imtech.res.in Wed Aug 19 08:12:37 2015 From: amanjain at imtech.res.in (amanjain at imtech.res.in) Date: Wed, 19 Aug 2015 17:42:37 +0530 Subject: [Bio-Linux] Bio-Linux Digest, Vol 83, Issue 7 In-Reply-To: References: Message-ID: <5c680b5a33905951a426f36d5eff582e@imtech.res.in> InterProScan is working properly. It was running fine with the example input file. If you wish you can access my system using TeamViewer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Wed Aug 19 08:33:10 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 19 Aug 2015 13:33:10 +0100 Subject: [Bio-Linux] Bio-Linux Digest, Vol 83, Issue 7 In-Reply-To: <5c680b5a33905951a426f36d5eff582e@imtech.res.in> References: <5c680b5a33905951a426f36d5eff582e@imtech.res.in> Message-ID: <55D47786.8010605@minke-informatics.co.uk> On 19/08/15 13:12, amanjain at imtech.res.in wrote: > InterProScan is working properly. It was running fine with the example > input file. If you wish you can access my system using TeamViewer. Hi, Amanjain. Email me details off-list and I'll take a look. 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 From rjohns03 at carc.unm.edu Wed Aug 19 17:07:28 2015 From: rjohns03 at carc.unm.edu (Ryan Johnson) Date: Wed, 19 Aug 2015 15:07:28 -0600 Subject: [Bio-Linux] Bio-Linux server to submit to Ubuntu cluster Message-ID: <55D4F010.5010609@carc.unm.edu> Hello all, I have a cluster with 128 compute nodes that run vanilla Ubutnu 14.04 and a PBS/Torque system. We run Galaxy as a separate machine with Bio-Linux 8 (which can be though of as the Galaxy head node). Currently to make it work I have the following directories exported as NFS mounts into the cluster compute nodes: /etc/galaxy-server/ /var/lib/galaxy-server /usr/lib/galaxy-server We also have a cluster wide user called Debian-galaxy (which lives on the NIS *Yellow Pages*). Is this considered a safe and efficient way to operate our production Galaxy cluster? Thank you for your help! Regards, Ryan -- Ryan S. Johnson, PhD Applications Scientist Center for Advanced Research Computing P: (650) 430-6194 E: rjohns03 at carc.unm.edu From tony.travis at minke-informatics.co.uk Thu Aug 20 05:49:52 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 20 Aug 2015 10:49:52 +0100 Subject: [Bio-Linux] Bio-Linux server to submit to Ubuntu cluster In-Reply-To: <55D4F010.5010609@carc.unm.edu> References: <55D4F010.5010609@carc.unm.edu> Message-ID: <55D5A2C0.6030407@minke-informatics.co.uk> On 19/08/15 22:07, Ryan Johnson wrote: > Hello all, > > I have a cluster with 128 compute nodes that run vanilla Ubutnu 14.04 > and a PBS/Torque system. We run Galaxy as a separate machine with > Bio-Linux 8 (which can be though of as the Galaxy head node). Currently > to make it work I have the following directories exported as NFS mounts > into the cluster compute nodes: > > /etc/galaxy-server/ > /var/lib/galaxy-server > /usr/lib/galaxy-server > > We also have a cluster wide user called Debian-galaxy (which lives on > the NIS *Yellow Pages*). Is this considered a safe and efficient way to > operate our production Galaxy cluster? Hi, Ryan. There is no 100% safe way to operate a cluster if you expose the internal (cluster) network. I ran a Bio-Linux Beowulf with three separate network fabrics: System, Application and LAN. You should only export the NFS shares to cluster nodes on a private network and your NIS should be confined to the private network too. The design I used was based on EPCC (Edinburgh Parallel Computing Centre) BOBCAT (Budget Optimised Beowulf Constructed using Affordable technology). The most important/innovative aspect of BOBCAT was the separation of internal network fabrics for performance, but the same applies to separation of network fabrics for security reasons. HTH, 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 morais at iq.usp.br Thu Aug 20 12:02:06 2015 From: morais at iq.usp.br (Carlos Morais) Date: Thu, 20 Aug 2015 13:02:06 -0300 Subject: [Bio-Linux] Bio-Linux server to submit to Ubuntu cluster In-Reply-To: <55D5A2C0.6030407@minke-informatics.co.uk> References: <55D4F010.5010609@carc.unm.edu> <55D5A2C0.6030407@minke-informatics.co.uk> Message-ID: If you have no private network, I would recommend using IPSec On Thu, Aug 20, 2015 at 6:49 AM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 19/08/15 22:07, Ryan Johnson wrote: > > Hello all, > > > > I have a cluster with 128 compute nodes that run vanilla Ubutnu 14.04 > > and a PBS/Torque system. We run Galaxy as a separate machine with > > Bio-Linux 8 (which can be though of as the Galaxy head node). Currently > > to make it work I have the following directories exported as NFS mounts > > into the cluster compute nodes: > > > > /etc/galaxy-server/ > > /var/lib/galaxy-server > > /usr/lib/galaxy-server > > > > We also have a cluster wide user called Debian-galaxy (which lives on > > the NIS *Yellow Pages*). Is this considered a safe and efficient way to > > operate our production Galaxy cluster? > > Hi, Ryan. > > There is no 100% safe way to operate a cluster if you expose the > internal (cluster) network. I ran a Bio-Linux Beowulf with three > separate network fabrics: System, Application and LAN. You should only > export the NFS shares to cluster nodes on a private network and your NIS > should be confined to the private network too. > > The design I used was based on EPCC (Edinburgh Parallel Computing > Centre) BOBCAT (Budget Optimised Beowulf Constructed using Affordable > technology). The most important/innovative aspect of BOBCAT was the > separation of internal network fabrics for performance, but the same > applies to separation of network fabrics for security reasons. > > HTH, > > 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 > _______________________________________________ > 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 thackray at rci.rutgers.edu Fri Aug 21 13:48:32 2015 From: thackray at rci.rutgers.edu (Josh Thackray) Date: Fri, 21 Aug 2015 13:48:32 -0400 Subject: [Bio-Linux] tophat with -p > 1 results in missing reads Message-ID: <55D76470.2030106@rci.rutgers.edu> Hi All, I am running tophat (version 2.0.13, from the biolinux distribution). I am facing a problem where running tophat with increasing values for -p (number of threads) results in more and more reads lost in the final output. I'm starting with an uncompressed fastq file containing 18,115,321 reads, and running tophat with default parameters except for -p and -o. Running -p 8 results with the following information in align_summary.txt: Input : 318640 Mapped: 191949 (60.2% of input) of these: 29316 (15.3%) have multiple alignments (0 have >20) 60.2% overall read mapping rate. Running -p 4 results with the following information in align_summary.txt: Input : 1302700 Mapped: 759998 (58.3% of input) of these: 115861 (15.2%) have multiple alignments (1 have >20) 58.3% overall read mapping rate. Running -p 1 results with the following information in align_summary.txt: Input : 18115321 Mapped: 12014534 (66.3% of input) of these: 1867188 (15.5%) have multiple alignments (13 have >20) 66.3% overall read mapping rate. I also tried running tophat with the --no-sort-bam option to check if samtools was somehow screwing up during the mergesort operation, but I get the same result. I also confirmed the numbers reported in the align_summary.txt file using the samtools flagstat command. Further using bowtie1 instead of bowtie2 for the alignment engine did not resolve the problem of these reads going missing. Any ideas??? Thanks, Josh -- Josh Thackray Laboratory Researcher III Human Genetics Institute of NJ Department of Genetics Rutgers University From morais at iq.usp.br Mon Aug 24 15:48:17 2015 From: morais at iq.usp.br (Carlos Morais) Date: Mon, 24 Aug 2015 16:48:17 -0300 Subject: [Bio-Linux] Tophat Message-ID: Hi, I am using Bio-Linux repository on my Ubuntu Trusty. Tophat version is 2.0.13. When is the upgrade to 2.1.0 planned? Regards, Carlos -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Aug 25 06:56:27 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 25 Aug 2015 11:56:27 +0100 Subject: [Bio-Linux] tophat with -p > 1 results in missing reads In-Reply-To: <55D76470.2030106@rci.rutgers.edu> References: <55D76470.2030106@rci.rutgers.edu> Message-ID: <1440500187.5117.83.camel@wllt1771.nerc-wallingford.ac.uk> Hi Josh, This does look like a bug in Tophat. I'm working to push out the latest Tophat and Bowtie2 versions to the repository just now, to see if the issue is fixed: TopHat 2.1.0 Bowtie2 2.2.6 But the updated TopHat requires some extra Python libs, so I'm having to add them too and it takes a bit longer. I'll let you know when the update is ready. Cheers, TIM On Fri, 2015-08-21 at 13:48 -0400, Josh Thackray wrote: > Hi All, > > I am running tophat (version 2.0.13, from the biolinux distribution). I > am facing a problem where running tophat with increasing values for -p > (number of threads) results in more and more reads lost in the final > output. I'm starting with an uncompressed fastq file containing > 18,115,321 reads, and running tophat with default parameters except for > -p and -o. > > Running -p 8 results with the following information in align_summary.txt: > Input : 318640 > Mapped: 191949 (60.2% of input) > of these: 29316 (15.3%) have multiple alignments (0 have >20) > 60.2% overall read mapping rate. > > Running -p 4 results with the following information in align_summary.txt: > Input : 1302700 > Mapped: 759998 (58.3% of input) > of these: 115861 (15.2%) have multiple alignments (1 have >20) > 58.3% overall read mapping rate. > > Running -p 1 results with the following information in align_summary.txt: > Input : 18115321 > Mapped: 12014534 (66.3% of input) > of these: 1867188 (15.5%) have multiple alignments (13 have >20) > 66.3% overall read mapping rate. > > I also tried running tophat with the --no-sort-bam option to check if > samtools was somehow screwing up during the mergesort operation, but I > get the same result. I also confirmed the numbers reported in the > align_summary.txt file using the samtools flagstat command. Further > using bowtie1 instead of bowtie2 for the alignment engine did not > resolve the problem of these reads going missing. > > Any ideas??? > > Thanks, > > Josh > -- 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 paumarc at gmail.com Fri Aug 28 10:19:54 2015 From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=) Date: Fri, 28 Aug 2015 16:19:54 +0200 Subject: [Bio-Linux] port for ssh Message-ID: Hello Can any tell me which port should be used to connect via shh to biolinux?i found it is port 22, but it do not work for me pmunozt at home:~$ ssh paumarc at paumarc.zmm.irb.hr ssh: connect to host paumarc.zmm.irb.hr port 22: Connection timed out thanks Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Fri Aug 28 10:26:53 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 28 Aug 2015 15:26:53 +0100 Subject: [Bio-Linux] port for ssh In-Reply-To: References: Message-ID: <55E06FAD.2070605@minke-informatics.co.uk> On 28/08/15 15:19, Pau Marc Mu?oz Torres wrote: > Hello > > Can any tell me which port should be used to connect via shh to > biolinux?i found it is port 22, but it do not work for me Hi, Pau. The default port for SSH is 22, but you should check port 22 is open in your firewall or you won't be able to connect. HTH, 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 kirannbishwa01 at gmail.com Fri Aug 28 11:45:22 2015 From: kirannbishwa01 at gmail.com (Bishwa Kiran) Date: Fri, 28 Aug 2015 11:45:22 -0400 Subject: [Bio-Linux] Portable biolinux not booting in Dell inspiron 3000 Message-ID: I have been trying to install a portable bio-linux OS on external hdd. I have followed the instructions given for portable ubuntu/bilinux installation which has been sucessful and also made sure the boot/grub loader is installed in the external harddrive (seagate 2 tb) during installation. After the completion of bio-linux installation it requests the restart and biolinux boots up. But, after the 2nd boot the boot widow of biolinux gives me an error (that a USB-3 port is not available or is offline). I have installed biolinux several times thinking the installation may have missed the files but it always turns out the same way- 1st restart works but after the second restart/boot there is an error message. My desktop is Dell inspiron 3000 (i3) which by default uses UEFI boot system and I have disabled it while preparing the biolinux installation and have used legacy mode (modified BIOS setting). One interesting thing is that the same portable biolinux OS which didn't boot from desktop boots from my gateway laptop every time though. So, the problem basically is that the USB-3 port is not getting recognized while booting. I tried another USB-3 port which gave same error, all other USB 2 port however show biolinux OS loading (shows a loading Biolinux logo) but never fully boots even after 2-3 hours. I have been trying to make this work for 5 days now. I need to use this portable OS mainly on my desktop due it its higher performance and also I have to keep things running overnight. Any suggestions appreciated and thanks in advance. I took the picture of the error message. -- - Bish -------------- next part -------------- An HTML attachment was scrubbed... URL: