Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hello and MACS-1.4.2 installation questions

    Hey everyone! I just started processing fastq files, making .bam files, and now I'm working on installing and running MACS-1.4.2. As a newbie to this field as well as using a terminal on my Mac, I'm running into some issues and would like some help.

    I'm on step 3 of installation (here is a link to the installation procedure: http://www.nature.com/nprot/journal/...html#procedure) and I cannot successfully execute the script provided after navigating to the appropriate directory. The previous step was successful in that I was able to download the .tar.gz file and unpack it.

    Here's the script that I'm having issues running: > python setup.py install

    Here's what I get (sorry for the excessive length):
    /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'console'
    warnings.warn(msg)
    running install
    error: can't create or remove files in install directory

    The following error occurred while trying to add or remove files in the
    installation directory:

    [Errno 13] Permission denied: '/Library/Python/2.7/site-packages/test-easy-install-5525.write-test'

    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:

    /Library/Python/2.7/site-packages/

    Perhaps your account does not have write access to this directory? If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account. If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.

    For information on other options, you may wish to consult the
    documentation at:



    Please make the appropriate changes for your system and try again.


    I've gone to the website specifying how to install/use Easy Install, but it is incredibly non-user friendly, and as a scientist without much coding background, I found it hard to comprehend the instructions to install Easy Install, let alone actually do it.

    When I try the alternative installation script, > python setup.py install --prefix /your_directory/

    I get: [Errno 2] No such file or directory:your_directory

    At this point, I've tried various paths, just in case the one I specify is incorrect, and have had no luck.

    Has one else here had similar issues installing MACS-1.4.2? Any advice?

    Thanks!

    Uchillama from VA

  • #2
    Do you have admin access to this Mac? If you do then try

    Code:
    $ sudo python setup.py install
    You will have to provide the password for admin account. See if that fixes the problem.

    Unless you have a specific reason to use the older MACS you probably should install MACS2 from here: https://github.com/taoliu/MACS/wiki/Install-macs2

    Comment


    • #3
      The code worked! Thanks so much!

      Are there any specific reasons to use MACS2 over MACS1? The only reason I'm using MACS1 is because a collaborator uses it as well, which I realize isn't the best reason.

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X