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Requirements

  • Operating systems: Unix, OSX
  • Python >=2.7

Python modules (installed via setup.py):

  • Numpy (>=1.7.0)
  • BioPython (>=1.6.2)
  • Pysam (>=0.8.1)
  • Pandas (>=0.17.1)

External binaries (included with package):

  • Bowtie2 (2.3.2)
  • samtools (1.4)
  • hs-blastn

Speed and memory usage

Most steps of the program are quite fast, require < 2Gb of RAM, and are compatible with multithreading. For a typical gut metagenome, expect ~30 minutes for species profiling and 60-90 minutes each for calling nucleotide and gene copy number variants.

Download the software

Clone the latest version from GitHub (recommended):
git clone https://github.com/snayfach/MIDAS
This makes it easy to update the software in the future using git pull as bugs are fixed and features are added

Or, download the latest source code, and unpack the project: unzip MIDAS-master.zip

Or, download a stable release of the source code:
https://github.com/snayfach/MIDAS/releases

Install dependencies

The dependencies can be installed by running the setup.py script:
python MIDAS/setup.py install or
sudo python MIDAS/setup.py install to install as a superuser, or
python MIDAS/setup.py install --user to install locally

Or, if you have pip installed, you can install these dependencies by running the following command:
pip install -U numpy biopython pysam pandas or
sudo pip install -U numpy biopython pysam pandas to install as a superuser, or
pip install --user numpy biopython pysam pandas to install locally

If you run into problems, check out these additional instructions:
Installing MIDAS on Mac OS X 10.11 and later
Installing on CentOS/Ubuntu

If you still have installation issues, please open a new issue on GitHub

Update your environmental variables

This will enable you to run MIDAS scripts:
export PYTHONPATH=$PYTHONPATH:/path/to/MIDAS
export PATH=$PATH:/path/to/MIDAS/scripts
export MIDAS_DB=/path/to/midas_database

Be sure to replace '/path/to' with the appropriate path on your system
Add these commands to your .bash_profile to avoid entering the commands in the future

To learn how to download the default MIDAS database, click here
To learn how to build your own MIDAS database, click here

Testing

Run the following command to test MIDAS:
cd /path/to/MIDAS/test
test_midas.py -vf

This will take a few minutes to complete. If you don't have VSEARCH and HMMER installed, the last test (for building a custom database) will fail. This is OK and will not affect the rest of the program.

If you do want to test the database building module, you'll need to add HMMER and VSEARCH installation directories to your PATH:
export PATH=$PATH:/vsearch/installation/directory
export PATH=$PATH:/hmmer/installation/directory

Update MIDAS

MIDAS changes over time as new features are added and bugs are fixed

To update MIDAS, move to installation directory and pull the latest version:
cd MIDAS
git pull

Or, download the latest stable release of the source code:
https://github.com/snayfach/MIDAS/releases

To be notified of these changes, click the "Watch" button in the upper right corner of the page, or sign up for the mailing list

Next step

Step-by-step tutorial