ILRI Research Computing

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====== FragGeneScan ======
FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. 

===== Information =====

  * Version: 1.30
  * Added: July, 2015
  * Updated: March, 2020
  * Link: https://omics.informatics.indiana.edu/FragGeneScan/

===== Usage =====

See versions of FragGeneScan which are available:
<code>$ module avail fraggenescan</code>

Load one version into your environment and run it:

<code>$ module load fraggenescan/1.30
$ run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] -thread=[num_thread]</code>

**Note:** Please remember to specify the same number of CPU threads as you have requested in your SBATCH job parameters.

===== Installation ======
Notes from the sysadmin during installation:

<code>
$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/fraggenescan/FragGeneScan1.30.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Ffraggenescan%2Ffiles%2FFragGeneScan1.30.tar.gz%2Fdownload&ts=1584261823' -O FragGeneScan1.30.tar.gz
$ tar xf FragGeneScan1.30.tar.gz 
$ cd FragGeneScan1.30
$ scl enable devtoolset-7 bash
$ make clean
$ make fgs
$ sudo mkdir -p /export/apps/fraggenescan/1.30
$ chmod 644 example/* train/* *.h *.c
$ sudo cp -r . /export/apps/fraggenescan/1.30
</code>