Hi Everyone –

 

A new batch of software has been installed on premise.  The full list is included at the end of this email. 

 

Additionally, both the QIIME and QIIME2 pipeline packages have been installed.  Due to installation requirements, they are run in a different manner than other COLSA premise software:

 

  1. Unload the linuxbrew/colsa module (if loaded): “module unload linuxbrew/colsa”
  2. Load the anaconda/colsa module: “module load anaconda/colsa”
  3. Activate the desired QIIME environment: “source activate qiime1” or “source activate qiime2”
  4. Execute the desired QIIME commands
  5. When done:
    1. If finished with session, simply logout
    2. To continue working with other COLSA software, deactivate the QIIME environment: “source deactivate”
    3. Unload anaconda module: “module unload anaconda/colsa”

 

Also, we’ve gotten a few requests on where program-packaged data files (such as Augustus’s config/profile/model files) are located on premise.  These can usually be found in the following location:

 

/mnt/lustre/software/linuxbrew/colsa/Cellar/<PROGRAM NAME>/<VERSION>/

 

Often, they will be located in the “libexec” subdirectory in this location. Note, these directories are read only.  If you require modifying a file (such as a customized configuration file), copy the file into your home directory and instruct the application to make use of this location. 

 

The newest software list is as follows:

 

·  linuxbrew/colsa -- A collection of the following bioinformatics software:

·  anaconda/colsa -- A collection of the following bioinformatics software:

Thanks -

 

Toni Westbrook

Computational Scientist

Research Computing Center, College of Life Sciences and Agriculture

University of New Hampshire

Offices: 219 Morse Hall, 436 Gregg Hall