Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • HESmith
    replied
    Follow up: apparently, Autotools was dropped by Apple due to GPLv3 licensing issues. Also, gcc in current Xcode is actually a symlink to llvm-gcc (which doesn't have the licensing issue).

    -Harold

    Leave a comment:


  • HESmith
    replied
    FYI, the latest version of Xcode doesn't include some standard GNU compiling components (e.g., automake, autoconf, libtools), even after installing the Command Line Tools as suggested.

    -Harold

    Leave a comment:


  • ChrisBird
    replied
    Solution to make: command not found

    If you have OSX Lion, then Xcode does not automatically install the command line tools.

    When trying to install SAM Tools using Make, you will get the error message that make isn't found.

    You have to open Xcode, goto Preferences/Downloads, and then install the command line tools.

    Leave a comment:


  • mbblack
    replied
    Originally posted by kriskris View Post
    I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

    Thanks!
    Strictly speaking, XCode is not necessary, but you need a gcc compiler and tools in order to compile Samtools. There are open source tools available for OS X, but by far the simplest to set up would be to spring for XCode and install it.

    XCode is only available from Apple, either through the App store or by paying to register as a developer.

    Leave a comment:


  • maubp
    replied
    Originally posted by kriskris View Post
    I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

    Thanks!
    It used to be on the DVD that came with your Mac.

    Leave a comment:


  • Wallysb01
    replied
    Xcode for OSX 10.6 is $5, I think. Its free if you have OSX 10.7. You can still download Xcode 4 for 10.6, and you will need it for samtools or any program that requires a "make" command.

    Leave a comment:


  • kriskris
    replied
    I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

    Thanks!

    Leave a comment:


  • maubp
    replied
    Have you installed Apple's Xcode? That provides gcc, make, etc. Get it free from the Apple App Store (big download).

    Leave a comment:


  • kriskris
    started a topic Installing Samtools on MacOS

    Installing Samtools on MacOS

    Hi,

    I'm trying to install samtools on my Mac (OS X 10.6.8). I downloaded samtols-0.2.1.18tar.bz2 and unzipped it on my desktop. Then in terminal, I entered that directory and typed "make". It says "command not found".

    I saw that zlib is required, so I also downloaded that and put the samtools into that directory and tried typing "make", which gave the same "command not found" message.

    I'm new to unix but have successfully installed and used other programs (Bowtie, etc.), so I'm not sure why I'm having such problems with Samtools.

    Any help would be greatly appreciated!

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:58 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
182 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:18 AM
0 responses
231 views
0 likes
Last Post seqadmin  
Working...
X