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Installing Newbler 2.5.3 on 64 bit Ubuntu...anyone???

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  • Dane
    replied
    I installed a new directory for a "local" install rather than system. So the new directory is home/dane/454/

    The old directory is still in opt/454/bin with all the files.

    64bit Ubuntu, Im not sure which package the installer used. However, I tried replacing any of the i686 tarballs that might have been installed instead of the x86 and then the programs wouldn't assemble and would come up with syntax errors.

    Leave a comment:


  • sklages
    replied
    Originally posted by Dane View Post
    The data analysis pkg

    When i use the "sfffile -i mapped.txt -o mapped.sff ../sff/*" command it returns that the "command doesnt exist"



    I don't understand how to recode the path for the sfffile. It looks like its trying to use an old folder for the sfffile command.

    This is what the terminal is spitting out:
    bash: /path/to/roche/datanalysis/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/454/bin: No such file or directory


    If you could give me specifics that would be appreciated since I still dont understand Ubuntu all that great yet.
    Here may be the problem, you should replace the path "/path/to/roche/datanalysis/bin" with the real bin path,
    I suspect this is "/opt/454/bin".
    So you need to export this path,

    export PATH="/opt/454/bin:$PATH"

    on the other hand, /opt/454/bin has already been there.
    Have you installed the software to /opt/454?

    Have a look at /opt/454/bin and see what's inside,

    ls /opt/454/bin/

    Do you see all programs?

    Is this a 64bit or 32bit Ubuntu? Did you install the correct i686 or x86_64 package?

    cheers,
    Sven

    Leave a comment:


  • Dane
    replied
    Originally posted by sklages View Post
    What did you install (what is the "new software")? sfffile is part of the DataAnalysis package.
    Sven
    The data analysis pkg

    Originally posted by sklages View Post
    What does it mean that you are "not able to use the sfffile command in the
    terminal"?
    Sven
    When i use the "sfffile -i mapped.txt -o mapped.sff ../sff/*" command it returns that the "command doesnt exist"

    Originally posted by sklages View Post
    You should probably set your (command) PATH (use your installation path):

    export PATH="/path/to/roche/datanalysis/bin:$PATH"

    and then type 'sfffile'.

    To make this permanent use e.g. .bashrc

    Sven
    I don't understand how to recode the path for the sfffile. It looks like its trying to use an old folder for the sfffile command.

    This is what the terminal is spitting out:
    bash: /path/to/roche/datanalysis/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/454/bin: No such file or directory


    If you could give me specifics that would be appreciated since I still dont understand Ubuntu all that great yet.
    Last edited by Dane; 03-08-2011, 09:15 AM.

    Leave a comment:


  • sklages
    replied
    Originally posted by Dane View Post
    I have installed the new software successfully but am now not able to use the sfffile command in the terminal, anyone else having this problem and know an easy fix?
    What did you install (what is the "new software")? sfffile is part of the DataAnalysis package.

    What does it mean that you are "not able to use the sfffile command in the
    terminal"?

    You should probably set your (command) PATH (use your installation path):

    export PATH="/path/to/roche/datanalysis/bin:$PATH"

    and then type 'sfffile'.

    To make this permanent use e.g. .bashrc

    Sven

    Leave a comment:


  • Dane
    replied
    I have installed the new software successfully but am now not able to use the sfffile command in the terminal, anyone else having this problem and know an easy fix?

    Leave a comment:


  • jvhaarst
    replied
    I have done a quick analysis of the basecalling differences between 2.3 and 2.5.3:


    The higher resolution pdf (with summary information on the reads) is available at http://db.tt/gbL9pYi

    Leave a comment:


  • sklages
    replied
    In every installer of every version of the roche suite, they always introduce something weird, to remove it in the next version of the installer .. take a bet that in the next major release of the suite 'rocks' has been eliminated (but something new has been introduced) ..

    SCNR,
    Sven

    Leave a comment:


  • rad
    replied
    Assuming you have a bin directory in your $HOME, and its in your $PATH

    ln -s /bin/true ~/bin/rocks

    then run the installer.

    Leave a comment:


  • Abbe
    replied
    Installing Newbler 2.5.3 on 64 bit Ubuntu

    We just did it!

    It took us 45 min.Thanks for the installation instruction.

    Leave a comment:


  • jvhaarst
    replied
    The Data Processing rpm's can be 'installed' like this:

    First download the DataProcessing_2.5.3.tgz file.
    Extract that file in a place of your liking.

    In a terminal, go to the directory packages of the extracted file, and do this :

    for file in gsReporter-2.5.3-1.x86_64.rpm gsRunBrowser-2.5.3-1.i686.rpm gsRunProcessor-2.5.3-1.x86_64.rpm gsSupportTool-1.23-1.i386.rpm;do rpm2cpio $file | cpio -idmv ; done

    This will extract the contents of all the RPMs in the local directory, in a /opt subdirectory.
    Now simply move the different applications to the place where you want them, like this :

    mv -v ~/bin/454_2.5.3/DataProcessing_2.5.3_All/packages/opt/454/apps/* ~/bin/454_2.5.3/apps/

    Then create links for the applications on a spot in your path :

    cd ~/bin/454_2.5.3/bin ; ln -vs ../apps/gs*/bin/* .

    Leave a comment:


  • just_testing
    replied
    Thank you for manual installation instructions. I tried to follow them but still can't get gsAmplicon to work properly, the GUI does launch but then it won't create a new project and trying to open an old project results to an empty error dialog. Has anyone else tried to use gsAmplicon with this installation?

    Leave a comment:


  • WaltL
    replied
    Installation of Newbler version 2.5.3 on Ubuntu 10.04.1 (Lucid Lynx) without using the supplied Nixstaller.

    Important Note: Do not cut and paste the commands below. Type them in.

    Important Note 2: This installation should also work with earlier versions of Ubuntu. Later versions of Ubuntu, 10.04.1 and 10.10 (Maverick Meerkat), did not come with Sun java as did previous versions. I have also tested this installation using java-6-openjdk that comes with 10.04 and 10.10 and it works just fine.

    I'm sure there are probably easier/faster ways to accomplish this install, however, this is a tested work around and I have tried and tested. I wrote this with detailed instructions so that those with little or limited unix/linux experience should be able install Newbler without too much difficulty.

    My apologies to those who find the step by step approach to be over-kill.


    1) Everything needs to be done with root privileges so it's easier to just become root (if you can't this, better stop now and get someone to help you with the install).

    2) If you have Newbler already installed, rename the directory opt/454 to something like opt/454_older.ver.number and go to step 3.

    If Newbler has never been installed, you will also need to add opt/454/bin to your path. Different ways to do this. I did it by creating an .sh file that contains the path and placing the file in /etc/profile_d
    Example:
    /etc/profile_d~# pico -w 454.sh

    Once in the pico editor type the following:

    export PATH=$PATH:/opt/454/bin

    exit editor with CtrlX and yes to save. You will need to log off and then log back on for the path change to take place.
    Now open a bash shell and enter echo $PATH at the prompt to verify that the path has been added and become root again.

    3) Navigate to the indicated directories below and create the following directories in the indicated locations:

    opt/~# mkdir 454
    opt/454~# mkdir apps
    opt/454/apps~# mkdir jre

    4) Copy the Newbler tarball file DataAnalysis.tgz to directory /opt/454 and extract (either at command line using tar -xzvf DataAnalysis.tgz or with the Ubuntu GUI package manager)

    5) Remove the file DataAnalysis.tgz after you have extracted it.

    6) Navigate to the directory DataAnalysis_2.5.3/packages/ and copy the following .tgz files to the indicated destinations:

    /opt/454/DataAnalysis_2.5.3/packages~# cp newbler_CLI-2.5.3.x86_64.tgz ../../
    /opt/454/DataAnalysis_2.5.3/packages~# cp assembly_GUI_2.5.3.noarch.tgz ../../apps
    /opt/454/DataAnalysis_2.5.3/packages~# cp mapper_GUI_2.5.3.noarch.tgz ../../apps
    /opt/454/DataAnalysis_2.5.3/packages~# cp amplicon_GUI_2.5.3.noarch.tgz ../../apps

    7) Navigate to the directories shown below and extract the the four tarballs. You should remove each .tgz file after extracting it.

    opt/454~# tar -xzvf newbler_CLI-2.5.3.x86_64.tgz
    opt/454/apps~# tar -xzvf assembly_GUI_2.5.3.noarch.tgz
    opt/454/apps~# tar -xzvf mapper_GUI_2.5.3.noarch.tgz
    opt/454/apps~# tar -xzvf ampicon_GUI_2.5.3.noarch.tgz

    8) Now remove the directory DataAnalysis_2.5.3 located in opt/454

    If you've done everything correctly to this point, your directory structure will look like this:

    /opt/454~# ls
    apps bin config

    /opt/454/apps~# ls
    amplicons assembly jre mapper


    Now we need to make multiple symbolic links to get everything to run. You can do this two ways:

    A) Use the command gksudo nautilus which opens a GUI with root privileges and then create the the required symbolic links graphically by copying and pasting the target link to its appropriate destination directory.
    B) Make the symbolic links at command line (as I have shown).


    First make the primary java link:

    9) Navigate to the directory /opt/454/apps/jre and create a symbolic link to the java that Ubuntu is using and give it the name of the java directory that Newbler wants to use: jre1.6.0_13
    Use either A or B, not both!

    A) For early Ubuntu versions with Sun Java

    /opt/454/apps/jre~# ln -s /usr/lib/jvm/java-6-sun jre1.6.0_13

    B) For later Ubuntu versions without Sun Java installed:

    /opt/454/apps/jre~# ln -s /usr/lib/jvm/java-6-openjdk jre1.6.0_13

    You can check that the link was made by doing an ls command and you should see one of the following:
    jre1.6.0_13 -> usr/lib/jvm/java-6-sun/ OR jre1.6.0_13 -> usr/lib/jvm/java-6-openjdk/


    Now, you need to make symbolic links for the three applications (amplicon, assembly, and mapper) back to the link that you just created in /opt/454/apps/jre
    (again, you can also do this in Nautilus by just copying the link you created in opt/454/apps/jre and then pasting into the appropriate directories below)

    10) Navigate to the directories shown below and create the symbolic link in each as follows:

    /opt/454/apps/assembly/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
    /opt/454/apps/amplicon/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
    /opt/454/apps/mapper/jre~# ln -s ../../jre/jre1.6.0_13 jre1.6.0_13

    Again, an ls command from within each jre directory should show the following:
    jre1.6.0_13 -> ../../jre/jre1.6.0_13

    Now you need to create the final four symbolic links, these are all from within the /opt/454/bin directory, to the their respective application executables which listed below:
    1) /opt/454/apps/assembly/bin/gsAssembler
    2) /opt/454/apps/mapper/bin/gsMapper
    3) /opt/454/apps/amplicon/bin/gsAmplicon
    4) /opt/454/apps/amplicon/bin/doAmplicon


    11) Navigate to opt/454/bin and create the following symbolic links:

    /opt/454/bin~# ln -s ../apps/assembly/bin/gsAssembler gsAssembler
    /opt/454/bin~# ln -s ../apps/mapper/bin/gsMapper gsMapper
    /opt/454/bin~# ln -s ../apps/amplicons/bin/gsAmplicon gsAmplicon
    /opt/454/bin~# ln -s ../apps/amplicons/bin/doAmplicon doAmplicon


    12) Test each program at command line by typing the program name, e.g. gsAssemble, gsMapper, or gsAmplicon.

    In each case the GUI should launch. If it doesn't, it is likely due to an error in creation of the symbolic links for either java or the executables.
    Note: that doAmplicon is a command line program and does not launch a GUI but goes to a > prompt.

    Happy Assembling!

    Leave a comment:


  • WaltL
    replied
    I worked on it most of the day and finally got it installed.

    It is not too difficult, but you cannot use the installer. I am performing a test assembly this morning and I will post installation instructions a bit later today.

    Walt

    Leave a comment:


  • sklages
    replied
    ... might be overkill .. but the result is what count :-)
    - install a redhat in a virtual machine
    - install roche newbler on the redhat system
    - copy the roche directory tree on your "working" system

    Usually Roche's installer is a catastrophe; changing though from version to version .. :-)

    my 2p,
    Sven

    Leave a comment:


  • ulz_peter
    replied
    I got the very same problem. I didn't resolve it (my knowledge of shell scripting is limited...). I resolved another error where Nixstaller tried to find lspci under /sbin which is under /usr/bin in Ubuntu but the type rocks problem didn't change...

    Maybe I'll switch to a ReHat derived distribution as the Roche engineers seem to only bear that in mind.

    Leave a comment:

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