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This is a tutorial in setting up SURPI pipeline on CentOS

SURPI is a pipeline to findout the pathogens from clinical metagenomics samples. It is tested only on Ubuntu and it assumes many things about your installation.

The github page of SURPI https://github.com/chiulab/surpi.

Make sure:

  1. The create_snap_to_nt.sh program uses -Ofactor as 1000, on line 29, which may not work for your machine. You need to figure out the correct value and make necessary changes.
  2. The abyss instalation requires mmap. Make sure you have installed it. http://hackage.haskell.org/package/mmap-0.5.9/mmap-0.5.9.tar.gz
  3. Make sure formatdb is there in your path. It can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/
  4. The taxonomy_lookup.pl program, at line 84 has sort --parallel=$cores, where you may need to remove --parallel=$cores option, if the sort utility on you machine does not support --parallel option.
  5. The abyss_minimus.sh program tries to use mpirun to make it parallel. If the mpirun is not configured properly, you need to remove the option 'np=$cores' in line 86, so that it will not be run parallelly.
  6. The ribo_snap_bac_euk.sh program is hardcoded to use the 10,75 as arguments to crop_reads.csh, which you may need to change in line 43.
  7. The coveragePlot.py program uses mlab.load() at line 47, which is deprecated in latest version of matplotlib. Hence, you may need to change it to np.load()