Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • mido1951
    replied
    resolved!
    best link

    Leave a comment:


  • GenoMax
    replied
    @mido1951: Since you are posting in multiple threads I will just use this one for. The "error" you are posting is a "warning" so it is possible that you have newbler installed. You should go ahead and try to run a test data set (not sure if one is included in newbler) and show us any additional errors (if they show up).

    Leave a comment:


  • mido1951
    replied
    Originally posted by crusoe View Post
    Thanks, this worked for me on Ubuntu 12.04.1 w/ Newbler 2.8
    How did you do to run Newbler ubuntu 14.04 ?
    thankyou

    Leave a comment:


  • hemant
    replied
    i was able to install newbler 2.8 on my Ubuntu desktop.

    following the dash and bash command from


    it looks like it is running properly.

    If I copy all the installation folders to cluster (supercomputer) (in my folder - local installation) will I be able to run the programme on my cluster.

    I was trying this by typing
    export PATH=/home/username/454/bin:$PATH
    $ newAssembly test

    but the folder (test) was not being created.

    Am I doing this the wright way.

    Leave a comment:


  • cement_head
    replied
    Newbler GUI is 32 Bits. Their packages install without errors if you have the ia32 libraries. I know this, because I called and spoke with Roche 454 technical support.

    Maybe try reinstall with the 32 bit libraries and see if the errors go away?

    Leave a comment:


  • sklages
    replied
    Originally posted by cement_head View Post
    Hi,

    As per the first line of the instructions - you MUST have the ia32 libraries installed for the GUI's to work. Newbler is actually 64bit software, but the GUI's are 32 bit, so unless you want to use only CLI (Command Line Interface), you'll need to install the ia32 libraries.
    We always run Newbler on 64bit systems, never installed ia32 libs.
    Newbler ships with its own version of GUI libs (hmm, java).
    The warning occurs during installation, yes, but never had any side effects (here).
    Time for Roche to clean up their code / installation packages :-)

    Leave a comment:


  • cement_head
    replied
    Probably not - contact the Cluster Admin - he/she can install it for you.

    Leave a comment:


  • GenoMax
    replied
    Originally posted by hemant View Post
    can i install it by myself in my folder in the cluster

    and how do i install ia32 libraries
    If you do not have "sudo" rights on this system you are probably not going to get much further with the ia32 library/newbler install. Are you not able to call on an administrator to help with the install?

    Leave a comment:


  • hemant
    replied
    can i install it by myself in my folder in the cluster

    and how do i install ia32 libraries
    Last edited by hemant; 02-21-2013, 07:58 AM.

    Leave a comment:


  • cement_head
    replied
    Originally posted by hemant View Post
    The sudo comand does not work for me when i was trying to install newbler 2.8

    can u give a step by step method for new installation.
    I tried tha bash setup.sh command but it gave some message that "one or more of the following library were not found zlib.i386, libxi.i386, libxtst.i386, libxav.i386 without these library 454 software may not run properly".


    Can anyone please help
    Hi,

    As per the first line of the instructions - you MUST have the ia32 libraries installed for the GUI's to work. Newbler is actually 64bit software, but the GUI's are 32 bit, so unless you want to use only CLI (Command Line Interface), you'll need to install the ia32 libraries.

    GenoMax is correct - you must have "Super User" DO privilidges (sudo) to perform these commands. Only your system admin can do this. If you are your sys admin and you've forgotten your sudo password, you can reset it.

    HOWEVER, RESETTING YOUR SUDO PASSWORD IF YOU ARE NOT THE SYS ADMIN CAN BE CONSIDERED A MISSUSE OF COMPUTING RESOURCES AND MAYBE GROUNDS FOR TERMINATION. PLEASE CHECK WITH YOUR INSTITUTIONS CODE OF CONDUCT.

    Regards,
    CH

    Leave a comment:


  • GenoMax
    replied
    Originally posted by hemant View Post
    The sudo comand does not work for me when i was trying to install newbler 2.8


    Can anyone please help
    The system administrators have to give your account permission to run "sudo". Access to "sudo" gives your account some special rights. I assume you are not the administrator of this machine. You may need to work with an administrator to get access to "sudo" or you can ask them to do the install.

    Leave a comment:


  • hemant
    replied
    newbler 2.8 ?????

    The sudo comand does not work for me when i was trying to install newbler 2.8

    can u give a step by step method for new installation.
    I tried tha bash setup.sh command but it gave some message that "one or more of the following library were not found zlib.i386, libxi.i386, libxtst.i386, libxav.i386 without these library 454 software may not run properly".


    Can anyone please help
    Last edited by hemant; 02-21-2013, 07:33 AM.

    Leave a comment:


  • IanAWarren
    replied
    We also installed version 2.8 on BioLinux 6 using the above information.

    Thank you for the post!

    Leave a comment:


  • crusoe
    replied
    Thanks, this worked for me on Ubuntu 12.04.1 w/ Newbler 2.8

    Leave a comment:


  • Newbler 2.7 on BioLinux 7.0 (Ubuntu 12.04.1 LTS)

    1
    Yes
    100.00%
    1
    No
    0.00%
    0

    The poll is expired.

    Hello,

    I've just installed Roche's Newbler 2.7 on BioLinux 7.0. BioLinux 7.0 is Ubuntu 12.04 LTS (AMD64) with a "layer" on top of it. If you want to know how to do the BioLinux 7.0 install, it's pretty easy. See the following URL for more information:

    Code:
    http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
    Instructions for Installing Newbler 2.7:

    1) Make sure you have the ia32 libs installed.

    2) You can download the Newbler 2.7 RPMs from Roche.

    3) FOR RPM conversion:
    Code:
    sudo alien *.rpm --scripts

    4) Then install the freshly made DEBs.
    Code:
    sudo dpkg -i *.deb

    5) You'll have to manually create the gsAmplicons menu entry. The icon and executable will be in /opt/454 .

    Regards,
    CH
    Last edited by cement_head; 11-29-2012, 07:43 AM.

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X