Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • where to copy samtools binary to some directories

    I am installing cufflinks on my Mac OS X, and here is the instruction:



    Under Installing the SAM tools I follow the instructions below

    1. Download the SAM tools
    2. Unpack the SAM tools tarball and cd to the SAM tools source directory.
    3. Build the SAM tools by typing make at the command line.
    4. Choose a directory into which you wish to copy the SAM tools binary, the included library libbam.a, and the library headers. A common choice is /usr/local/.
    5. Copy libbam.a to the lib/ directory in the folder you've chosen above (e.g. /usr/local/lib/)
    6. Create a directory called "bam" in the include/ directory (e.g. /usr/local/include/bam)
    7. Copy the headers (files ending in .h) to the include/bam directory you've created above (e.g. /usr/local/include/bam)
    8. Copy the samtools binary to some directory in your PATH.

    I've done the fist 7 steps, but I am not sure how to proceed with the last step (#8): should I use the command:

    sudo cp -a samtools-0.1.18 /usr/local/

    or into some other directories? What does the PATH in step 8 indicate? Thanks!

  • #2
    PATH is a variable containing information on the directories that contain executable programs. If you type echo $PATH into your shell, it will spit the list out. Copy the file into one of those directories. You can also add new folders to your PATH, if you for some reason or another want the binary files in a specific location. You can google your way to how that is done, if youre interested.

    //A

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Investigating the Gut Microbiome Through Diet and Spatial Biology
      by seqadmin




      The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
      02-24-2025, 06:31 AM
    • seqadmin
      Quality Control Essentials for Next-Generation Sequencing Workflows
      by seqadmin




      Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

      Nucleic Acid Quality Control
      Preparing for NGS starts with isolating the...
      02-10-2025, 01:58 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-24-2025, 02:48 PM
    0 responses
    295 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-21-2025, 02:46 PM
    0 responses
    213 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-18-2025, 03:06 PM
    0 responses
    73 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-07-2025, 09:30 AM
    0 responses
    81 views
    0 likes
    Last Post seqadmin  
    Working...
    X