ILRI Research Computing

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====== MaxBin2 ======
MaxBin2 is the next-generation of [[https://sourceforge.net/projects/maxbin/|MaxBin]] that supports multiple samples at the same time. MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads.

===== Information =====

  * Version: 2.2.7
  * Added: March, 2020
  * Link: https://sourceforge.net/projects/maxbin2/

===== Usage =====

See versions of maxbin2 which are available:
<code>$ module avail maxbin2</code>

Load one version into your environment and run it:

<code>$ module load maxbin2/2.2.7
$ run_MaxBin.pl</code>

**Note:** Please use the ''-thread'' option to match the number of CPU threads requested in your SBATCH job parameters (default 1).

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

<code>
$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/maxbin2/MaxBin-2.2.7.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fmaxbin2%2Ffiles%2Flatest%2Fdownload&ts=1584261396' -O MaxBin-2.2.7.tar.gz
$ tar xf MaxBin-2.2.7.tar.gz 
$ cd MaxBin-2.2.7/src
$ scl enable devtoolset-7 bash
$ make
$ sed run_MaxBin.pl -i \
  -e 's/idba_ud/idba_hybrid/' \
  -e 's_IDBA\\-UD_IDBA\\-Hybrid_'
$ rm src/*.o
$ sudo cp -r *.hmm *.pl *.r src /export/apps/maxbin2/2.2.7
$ sudo chown -R root:root /export/apps/maxbin2/2.2.7
</code>

Note: according to the readme MaxBin2 needs IDBA-UD v1.1.1, but this version was published at least six years ago, after which time the binary was renamed to ''idba_hybrid''. Old tarballs are not available so I will try to see if patching ''run_MaxBin.pl'' to use the new ''idba_hybrid'' binary works...