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maxbin2-software [2020/03/15 09:51]
aorth created
maxbin2-software [2020/03/15 10:42] (current)
aorth
Line 16: Line 16:
  
 <code>$ module load maxbin2/2.2.7 <code>$ module load maxbin2/2.2.7
-</code>+$ 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 ====== ===== Installation ======
Line 23: Line 24:
  
 <code> <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>
  
-</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...
maxbin2-software.1584265910.txt.gz · Last modified: 2020/03/15 09:51 by aorth