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Elaina edited this page Dec 13, 2019 · 6 revisions

Install the latest stable version of the BinSanity suite of scripts via pip

$ pip3 install BinSanity
  • Before testing be sure you have all of the dependencies below installed

Dependencies

Prior to installation via pip be sure all dependencies are also installed.

Versions used at time of last update to script are provided in parenthesis.

Programs used to prepare input files for BinSanity and associated utility scripts include:

Installation of Dependencies

Install CheckM

  • CheckM
    • Follow installation insturctions found on the CheckM wiki
    • to download pplacer (a dependency of CheckM) follow the instructions here or do the following:
      • Go to the pplacer webpage and click on latest release. This will take you to the github page and contain source code. Download the file pplacer-linux-v1.1.alpha19.zip. In that file are pre-compiled version of pplacer, guppy, and rppr. The location of these need to be exported to your path.
$ export PATH=/LOCATION/OF/PPLACER/:$PATH

Install numpy

$ pip install numpy
  • If you recieve issues running BinSanity after installing numpy try rolling the distribution back to a previous version.

Install HMMER

  • HMMER can be downloaded like this:
$ wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz
$ tar -zxvf hmmer-3.1b2.tar.gz
$ cd hmmer-3.1b2
$ ./configure && make && sudo make install
$ cd easel && make check && sudo make install

Install featureCounts

  • To do this download the latest subread package (subread-1.x.x-source.tar.gz)
$ tar zxvf subread-1.*.*-source.tar.gz
$ cd subread-1.*.*-source/src
$ make -f Makefile.Linux ; cd ../
  • This will produce a directory called bin in the subread-1.x.x-source file containing the executables for featureCounts. These should be copied into your path.

Once Installed Run A Quick Test with the Infant Gut Assembly Provided on Github

The Infant Gut Metagenome collected and curated by Sharon et al. (2013) was clustered by us to test BinSanity. To confirm you have BinSanity working we have provided a folder Example containing the fasta file (INFANT-GUT-ASSEMBLY.fa) containing contigs for the Infant Gut Metagenome provided by Eren et al. (2015). All files associated with our BinSanity run are also provided, which includes the combined coverage profile (produced using Bowtie2 v2.2.5 on defaults, contig-coverage-bam.py, and cov-combine.py.

To run the test use the following command using the igm.fa and Infant_gut_assembly.cov.x100.lognorm

$ Binsanity -f . -l igm.fa -p -10 -c Infant_gut_assembly.cov.x100.lognorm

The output should be as follows:

       ******************************************************
        **********************BinSanity***********************
        |____________________________________________________|
        |                                                    |
        |             Computing Coverage Array               |
        |____________________________________________________|
        
        Preference: -10.0
        Maximum Iterations: 4000
        Convergence Iterations: 400
        Contig Cut-Off: 1000
        Damping Factor: 0.95
        Coverage File: Infant_gut_assembly.cov.x100.lognorm
        Fasta File: igm.fa
        Output directory: BINSANITY-RESULTS
        logfile: binsanity-logfile.txt

        (4189, 11)
        
       ______________________________________________________
      |                                                      |
      |                 Clustering Contigs                   |
      |______________________________________________________|
      Cluster 0: 5
      Cluster 1: 14
      Cluster 2: 75
      Cluster 3: 105
      Cluster 4: 54
      Cluster 5: 20
      Cluster 6: 34
      Cluster 7: 43
      Cluster 8: 27
      Cluster 9: 105
      Cluster 10: 35
      Cluster 11: 10
      Cluster 12: 39
      Cluster 13: 30
      Cluster 14: 727
      Cluster 15: 256
      Cluster 16: 574
      Cluster 17: 7
      Cluster 18: 620
      Cluster 19: 508
      Cluster 20: 350
      Cluster 21: 551

	  	Total Number of Bins: 22

         *|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*|*
         _____________________________________________________
        |                                                     |
        |                   Creating Bins                     |
        |_____________________________________________________|

         _____________________________________________________

                       Putative Bins Computed
                       in 233.362998962 seconds
         _____________________________________________________

Installing the latest Docker image

UNDER DEVELOPMENT, WILL BE UPDATED ASAP

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