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  • #16
    Hi :
    My solution for running a TS after failed to install on Ubuntu 12.04 and 10.04.
    -- run the vm ( ts 4 and ts 3.6 directly downloaded from ion community ) .
    First , I tested the vm on vm player ( free from vmware ).
    Now I have both TS 4 and TS 3.6 on vmware station 10 on my Ubuntu 12.04 server.
    Just an alternative. Hope this help.

    Comment


    • #17
      Originally posted by albert liu View Post
      Hi :
      My solution for running a TS after failed to install on Ubuntu 12.04 and 10.04.
      -- run the vm ( ts 4 and ts 3.6 directly downloaded from ion community ) .
      First , I tested the vm on vm player ( free from vmware ).
      Now I have both TS 4 and TS 3.6 on vmware station 10 on my Ubuntu 12.04 server.
      Just an alternative. Hope this help.
      Thank you for the reply, Albert!
      With vm I have a problem, too. I can't understand how to upload reads of Ion Torrent to the Torrent Server. On the site of ioncommunity I've read that raw data from sequencer will send to the server automatically. But I have only reads. So maybe you can tell me how to upload them to the VM and analyse?

      Comment


      • #18
        Hi Sacrolfur :

        -- Please note unless you are comfortable with ubuntu commands , you could mess up your TS server and your data.----

        What do you want from the vm ?
        1. reanalysed from previous run ( 1.wells Files )
        2. from raw data (DAT )
        What version of TS you are running now?
        With the TS 4 you should be able to export and import reports using web interface.
        This is the best way.
        ----------- Here is my experience and only for reference-------
        I had tried both raw data and reports ( 1.wells ) on my vm.
        due to some issues , I did not analyed from the raw data.
        Again, Here is my situation and solution.
        I need to reanalyse reports generated with 3.4 by 3.6.
        Since I just updated my TS to 4.
        I can only used the vm3.6 to do the job.
        -- Please note unless you are comfortable with ubuntu command , you could mess up your TS server and your data.----

        My host (Avatar)-ubuntu 12.04 server with NFS for data archive and storage.
        My guest (ts3.6 vm )
        ion torrent TS (G)-- connect to two NFS ( one is Avatar ) for reports storage.
        1. download vm3.6 from ion community

        2. run with vmware player /vmware workstation10
        configure sharing_folder on both host and guest
        guest(ts3.6vm) :
        mkdir vmsharing
        sudo mount -t vmhgfs .host:/ /home/ionadmin/vmsharing

        3. copy iondb from your Torrent server to vm3.6
        -- ssh into TS server with ionadmin and
        pg_dump -C -h localhost -U ion iondb > iondb.sql

        4. copy iondb.sql to vmsharing
        5. Stop vm torrent server background processes
        sudo /etc/init.d/ionCrawler stop
        sudo /etc/init.d/ionJobServer stop
        sudo /etc/init.d/ionPlugin stop
        sudo /etc/init.d/celeryd stop

        6. Switch users to postgres
        sudo su postgres
        7. restart postgres
        /etc/init.d/postgresql-8.4 restart
        8. dropdb iondb
        9. Create a new db
        psql <<- EOFdb
        CREATE DATABASE iondb;
        GRANT ALL PRIVILEGES ON DATABASE iondb to ion;
        \q
        EOFdb

        10. copy the iondb
        psql -U ion -d iondb -f iondb.sql
        11. restart vm and check with webbroswer to verify the db is updated
        12. update reference Hg19 , bed files and plugin
        copy hg19 folder from gandlaf to vm and upload beds

        13. rename /results/PGM_test to match your TS
        mv PGM_test snnnnnn
        14. copy reports to vm
        cp -R /home/ionadmin/vmsharing/*SN2* /results/analysis/output/Home/
        15. copy raw data to vm
        cp -R /home/ionadmin/vmsharing/R* /results/snnnnnn
        16. change the owner and group from ionadmin to www-data
        sudo chown -R www-data:www-data *

        --most information are from ion community --
        some modification for copy iondb
        hope this help.

        Comment

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