Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Diginorm Installation

    Hello,

    Does anyone have experience with installing Diginorm in a linux server without root access? The installation guide assumes you are using Amazon EC2 and have root access:


    I tried installing on a virtual box ubuntu machine where I had root access and I still ran into issues. When I ran ~/khmer/scripts/normalize-by-median.py it said that the khmer module could not be found. But running make for khmer didn't help. Seems like other people may have had issues installing as well:


    While trying to install on the server where I do not have root access I altered the paths but I suspect there may be some hard set paths in the installation files somehwere. Any help is much appreciated! Thank you.

  • #2
    Originally posted by rkizen View Post
    While trying to install on the server where I do not have root access I altered the paths but I suspect there may be some hard set paths in the installation files somehwere. Any help is much appreciated! Thank you.
    Yeah, the tutorial does not take some things into account...

    Anyway, since you do not have root permissions I do believe you have the PYTHONPATH variable with the location of the folder where you install your python libraries already exported. If you've already installed screed successfully, all you need to do is append the khmer path to the PYTHONPATH variable

    So you should have something like:
    export PYTHONPATH=/whatever/path/to/the/library/folder/

    Add:
    export PYTHONPATH=/whatever/path/to/the/library/folder/:/path/to/khmer/python/

    Note that "khmer/python" is in the folder which you cloned from github after the make test command. After you changed the bashrc or bash_profile, start a new terminal and try running the "/khmer/scripts/normalize-by-median.py" script and it should work.

    Hope this helps...
    Last edited by Guest; 08-16-2013, 07:21 AM.

    Comment


    • #3
      Thank you lorendarith. It seems to be working now. I wonder why the installation guide assumes you will have root access.

      Comment


      • #4
        I know that this is an old thread but as the lead developer on khmer I wanted to clear a few things up.

        Firstly, thanks for using our software!

        We've revamped the installation process considerably in the last year. I agree, assuming root access is not a good idea.



        I am very happy to help with any other khmer related issues. Alas I haven't found a way to receive an alert whenever someone mentions khmer on seqanswers. In the mean time please feel free to alert us via GitHub about any issues:

        In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more - Issues · dib-lab/khmer


        Or you can email us: [email protected]

        Cheers,

        Comment


        • #5
          Error in using normalize-by-median.py

          Hi, crusoe

          An error is coming while using normalize-by-median.py.

          python normalize-by-median.py -h

          Traceback (most recent call last):
          File "normalize-by-median.py", line 19, in <module>
          import screed
          ImportError: No module named screed

          If i am running any command also i am getting the same error. Is there any problem with python?

          Please help me..

          Thanks in advance..

          Comment


          • #6
            Hello amitbik,

            Looks like we resolved your problem over email. The next release of khmer included expanded installation instructions. They can be previewed at http://khmer.readthedocs.org/en/late...r/install.html

            Cheers,

            --
            Michael R. Crusoe

            Comment


            • #7
              Hi Crusoe

              Thanks a ton.. It is working fine now.... I will be waiting for next release of khmer.

              Cheers,
              --
              Amit

              Comment

              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
              32 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 10:19 PM
              0 responses
              35 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 09:21 AM
              0 responses
              29 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-04-2024, 09:00 AM
              0 responses
              53 views
              0 likes
              Last Post seqadmin  
              Working...
              X