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  • dschika
    replied
    Maybe this thread helps?
    http://seqanswers.com/forums/showthread.php?t=25339

    Leave a comment:


  • mido1951
    replied
    i have Ubuntu 12.04LTS.
    I installed the librairies ia32-libs.
    but it's the same problème.
    Thankyou

    Leave a comment:


  • GenoMax
    replied
    What flavor of unix/linux are you running?

    Here is a relevant thread that will help: http://ubuntuforums.org/showthread.php?t=1624351 See post #3.

    Leave a comment:


  • mido1951
    replied
    hello,
    I have a local installation of newbler but here the error message:

    Code:
    Warning: One or more of the following libraries was not found
    
       zlib.i386, libXi.i386, libXtst.i386, libXaw.i386
    
    Without these libraries, 454 Life Sciences software may not run correctly.  Consult the product documentation for more information.

    could you help me?
    thankyou

    Leave a comment:


  • yifangt
    replied
    Which one is the latest STLinux

    I saw this list, but which one should I pick?
    Code:
    stlinux24-host-STLinux_deps-20100401-1.i386.rpm 01-Apr-2010 17:01  4.2K  
    [   ] stlinux24-host-STLinux_deps-20100427-1.i386.rpm 28-Jun-2010 14:56  4.4K  
    [   ] stlinux24-host-STLinux_deps-20110126-1.i386.rpm 26-Jan-2011 11:47  4.4K  
    [   ] stlinux24-host-STLinux_deps-20110331-1.i386.rpm 31-Mar-2011 12:30  4.5K  
    [   ] stlinux24-host-STLinux_deps-20110614-1.i386.rpm 14-Jun-2011 10:40  4.5K  
    [   ] stlinux24-host-STLinux_deps-20111020-1.i386.rpm 20-Oct-2011 11:07  5.7K  
    [   ] stlinux24-host-STLinux_deps-20120508-1.i386.rpm 08-May-2012 14:20  5.7K  
    [   ] stlinux24-host-STLinux_deps-20120731-1.i386.rpm 01-Aug-2012 11:23  6.1K  
    [   ] stlinux24-host-STLinux_deps-20121030-1.i386.rpm 30-Oct-2012 14:41  7.1K  
    [   ] stlinux24-host-STLinux_deps-20130321-1.i386.rpm 21-Mar-2013 14:11  7.1K  
    [   ] stlinux24-host-STLinux_deps-20131122-1.i386.rpm 22-Nov-2013 13:43  7.1K  
    [   ] stlinux24-host-STLinux_deps-20140120-1.i386.rpm 23-Jan-2014 16:04  7.2K
    I assumed the last one,
    Code:
    stlinux24-host-STLinux_deps-20140120-1.i386.rpm
    and installed it. The problem is still there. Any idea? Thanks!

    Leave a comment:


  • justindyson
    replied
    I had the same issue. It's just because /bin/sh is not in the rpm database. To get round this I installed the STLinux "provides" RPM. This populates the database without installing anything and this happens to include /bin/sh:

    Information: http://stlinux.com/install/ubuntu
    Pick the latest version from here: http://download.stlinux.com/pub/stlinux/2.4/misc/

    Simply do a:

    Code:
    rpm -ivh --force-debian stlinux24<version>.rpm
    and then

    Code:
    sudo apt-get install ia32-libs
    sudo ln -s /bin/true /bin/rocks
    sudo ln -s /usr/bin/lspci /sbin/lspci
    sudo dpkg-reconfigure dash   (select no)
    sudo ./setup.sh
    It should install without any problems.

    Leave a comment:


  • JackieBadger
    replied
    http://seqanswers.com/forums/showthread.php?t=30045

    Leave a comment:


  • emq
    replied
    Hi brymerr,

    I am actually not sure but I think you have not to use
    HTML Code:
     sudo ./setup.sh
    . Try it without sudo, as my experience was that I could install 2.7 only locally and for this you don't need sudo.

    The link you created for bash did not work for root -- maybe.

    Leave a comment:


  • GenoMax
    replied
    That again looks right. Not sure what to ask you to try next. In case no one from the west coast helps further tonight we can look at this tomorrow.

    Leave a comment:


  • brymerr921
    replied
    Here is what appears:
    [email protected]:~$ echo $PATH
    /usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
    [email protected]:~$

    Leave a comment:


  • GenoMax
    replied
    That looks right. I wonder if you have a problem with your $PATH variable (i.e. /bin is not in that path, it seems unlikely).

    What is the output of

    Code:
    $ echo $PATH

    Leave a comment:


  • brymerr921
    replied
    I did the following commands:

    [email protected]:~$ sudo rm /bin/sh
    [sudo] password for bryan:
    [email protected]:~$ sudo ln -s bash /bin/sh
    [email protected]:~/Desktop/DataAnalysis_2.9_All$ ls -l /bin/sh
    lrwxrwxrwx 1 root root 4 Aug 12 19:35 /bin/sh -> bash

    I then tried to run setup.sh from Terminal and got the same error.

    Leave a comment:


  • GenoMax
    replied
    Did you try the code in post #5 from the thread that you have linked to? If you did then what do you see when you run the following?

    Code:
    $ ls -l /bin/sh

    Leave a comment:


  • brymerr921
    started a topic Install Newbler 2.9 in Ubuntu

    Install Newbler 2.9 in Ubuntu

    Hey everyone,

    I am trying to install the Data_Analysis2.9 package in Ubuntu 13.04. I am very new to Ubuntu and Newbler, but am trying to get this to work.

    Here is what I have done so far:
    1. Download DataAnalysis_2.9_All_20130530_1559.tgz
    2. Extract the *.tgz file to a folder on my desktop called "DataAnalysis_2.9_All"
    3. Open terminal, and run
    Code:
    sudo apt-get install ia32-libs
    4. From the bottom directory, type
    PHP Code:
    sudo ln -/bin/true /bin/rocks 
    (sudo ln -s /bin/true ~/bin/rocks didn't work.)
    5. Type
    Code:
    sudo apt-get install alien
    6. Type
    PHP Code:
    ln -/bin/sh 
    returns
    PHP Code:
    lrwxrwxrwx 1 root root 4 Aug 12 18:29 /bin/sh -> bash 
    7. In /Desktop/DataAnalysis_2.9_All, type
    PHP Code:
    sudo ./setup.sh 
    Then I get this error in the log file:
    Code:
    Installation started at 08/12/2013 06:45:41 PM
    
    User: uid=0(root) gid=0(root) groups=0(root)
    
    Hostname: bryan-ubuntu
    
    =============================
    [06:45:41 PM] cd /home/bryan/Desktop/DataAnalysis_2.9_All; md5sum -c checksum_inst
    
    ./setup.sh: OK
    ./README: OK
    ./packages/gsNewbler-2.9-1.x86_64.rpm: OK
    ./packages/amplicons_CLI_2.9.i686.tgz: OK
    ./packages/jre-linux-i586-oracle-2.9-1.i386.rpm: OK
    ./packages/gsNewbler-2.9-1.i686.rpm: OK
    ./packages/gsAssembler-2.9-1.noarch.rpm: OK
    ./packages/gsSeqTools-2.9-1.x86_64.rpm: OK
    ./packages/gsAmplicons-2.9-1.noarch.rpm: OK
    ./packages/gsSeqTools-2.9-1.i686.rpm: OK
    ./packages/gsMapper-2.9-1.noarch.rpm: OK
    =============================
    
    =============================
    [06:45:42 PM] rpm -U   --force  /home/bryan/Desktop/DataAnalysis_2.9_All/packages/jre-linux-i586-oracle-2.9-1.i386.rpm
    
    rpm: RPM should not be used directly install RPM packages, use Alien instead!
    rpm: However assuming you know what you are doing...
    warning: /home/bryan/Desktop/DataAnalysis_2.9_All/packages/jre-linux-i586-oracle-2.9-1.i386.rpm: Header V3 DSA/SHA1 Signature, key ID e50b562c: NOKEY
    =============================
    
    =============================
    [06:45:44 PM] rpm -U   --force  /home/bryan/Desktop/DataAnalysis_2.9_All/packages/gsSeqTools-2.9-1.x86_64.rpm
    
    rpm: RPM should not be used directly install RPM packages, use Alien instead!
    rpm: However assuming you know what you are doing...
    warning: /home/bryan/Desktop/DataAnalysis_2.9_All/packages/gsSeqTools-2.9-1.x86_64.rpm: Header V3 DSA/SHA1 Signature, key ID e50b562c: NOKEY
    error: Failed dependencies:
    	/bin/sh is needed by gsSeqTools-1:2.9-1.x86_64
    =============================
    This looks like the same error discussed at http://seqanswers.com/forums/showthread.php?t=20588, yet I can't get this to install. Thanks!

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