Difference: ProtocolsFlexbarCommands (10 vs. 11)

Revision 112014-08-12 - DanielDeatherage

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META TOPICPARENT name="ProtocolList"

Using Flexbar program to remove adapter sequences from NGS reads

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Installing Flexbar (notes specific to TACC, can be updated for other systems)

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Installing Flexbar on Mac.

 
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  1. Go to Flexbar home page select the newest version (2.31 as of 1-16-13).
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  1. Go to Flexbar home page select the newest version (2.5 as of 8-12-14).
  2. Download _macosx.tgz file.
  3. Move downloaded file to more permanent location (ie source)
  4. Extract downloaded file.
  5. Extracted folder should contain 3 things:
    1. README.txt
    2. flexbar
    3. libtbb.dylib
  6. copy flexbar to your path, or add extracted folder to path.
    • suggest copying to $HOME/local/bin
  7. modify your .profile ($HOME/.profile) to include the following if not included already
    1. export PATH=$HOME/local/bin:$PATH
    2. export DYLD_LIBRARY_PATH="PATH-TO-YOUR-EXTRACTED-FOLDER":$DYLD_LIBRARY_PATH
      • replace everything including the quotation marks with the actual location of your extracted folder.
  8. open new terminal and flexbar should be working

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).
 
  1. Right click *_linux64.tgz and select 'copy link location'.
  2. Log onto TACC
  3. cd $WORK/src
 
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