Difference: ProtocolsFlexbarCommands (12 vs. 13)

Revision 132014-08-31 - JeffreyBarrick

Line: 1 to 1
 
META TOPICPARENT name="ProtocolList"

Using Flexbar program to remove adapter sequences from NGS reads

Changed:
<
<

Installing Flexbar on Mac.

>
>

Installing the Flexbar Executable on Mac

 
  1. Go to Flexbar home page select the newest version (2.5 as of 8-12-14).
  2. Download _macosx.tgz file.
Line: 20 to 20
 
      • replace everything including the quotation marks with the actual location of your extracted folder.
  1. open new terminal and flexbar should be working

Added:
>
>

Installing Flexbar from the Source Code on Mac

 
Changed:
<
<

Installing Flexbar on TACC.

>
>
Last tested on 31 Aug 2014.
  1. Use MacPorts to install any programs you need.
    port install cmake
    port install tbb
  2. Download the source code.
    svn export https://svn.code.sf.net/p/flexbar/code/trunk Flexbar
    cd Flexbar
    svn export -r 14262 https://github.com/seqan/seqan/trunk/core/include
  3. Add certain headers to your path
    source /opt/local/bin/tbbvars.sh
  4. Compile:
    cmake .
    make
  5. Copy the flexbar executable to your $PATH. There is no need to worry about the libtbb.dylib location when flexbar is installed this way.

Installing Flexbar on TACC

 
  • Currently Flexbar is installed on TACC under the BioITeam, but is only accessable as a job (que or idev) on lonestar. Stampede requires running on head node (bad idea) or copying it to a local directory in your path. Below are instructions for installing it yourself instead.
  1. Go to Flexbar home page select the newest version (2.5 as of 8-12-14).
 
This site is powered by the TWiki collaboration platform Powered by Perl This site is powered by the TWiki collaboration platformCopyright ©2021 Barrick Lab contributing authors. Ideas, requests, problems? Send feedback