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2 Installation Conda
MetaSanity is now conda-installable and supports Conda ≥ 4.10.3.
If this is your first time installing MetaSanity, skip to the Install Environment step below.
Prior to installing the conda version, remove your previous MetaSanity installation.
- Delete the
MetaSanitydirectory and the database directory, if needed. - Delete the
metasanity_envpython virtual environment, if needed. - Remove the old symlinks to the
MetaSanity.pyscript and theMetaSanity/Accessories/directory, if needed. - Delete the MetaSanity docker image.
docker image rm cjneely10/metasanity:v0.1.2
Your system must support wget.
Ensure you have the conda package mamba installed in your (base) environment:
conda install mamba -n base -c conda-forge -yFrom within your (base) environment and within a drive that has >120GB of storage space available, run the following commands:
git clone https://github.com/cjneely10/MetaSanity.git
cd MetaSanity
mamba env create -f environment.yml
./conda-install.shIf you do not see the "Your installation is complete" message, there was an error in the installation.
After installation, a system-specific version of MetaSanity.py will be created in the build directory.
There will also be a databases directory present in the installation directory that contains the databases required to run MetaSanity.
Your ~/.bashrc file will be updated with the value GTDBTK_DATA_PATH. You must restart your bash session for these changes to take effect.
MetaSanity can integrate additional software into its pipeline. However,
Some optional programs in MetaSanity require users to accept additional academic license agreements.
-
SignalP4.1 may optionally be installed.
- SignalP is used in the annotation pipeline with PSORTb to predict the presence of signal peptides. If it is not included, some extracellular assignments may be missed.
- Accept the user-agreement and download.
- Follow the website's installation instructions.
-
RNAmmer1.2 may optionally be installed.
- RNAmmer may be used to detect ribosomal RNA genes (in place of the default Barrnap). Excluding it will not affect the analysis in any way.
- Accept the user-agreement and download.
- Follow the website's installation instructions.
- InterProScan-5.36-75.0 may optionally be installed.
- InterProScan predicts protein domains in the gene calls. Its use adds significant runtime to an analysis, but it can provide a significant increase in the total number of annotations.
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.36-75.0/interproscan-5.36-75.0-64-bit.tar.gz- Optional Panther database download instructions are available here.
- The precalculated match lookup is not supported. Change the line 239 in
interproscan.propertiesto beprecalculated.match.lookup.service.url=, or include the flag--disable-precalcwhen incorporating InterProScan in the FuncSanity workflow.
MetaSanity is run using the MetaSanity.py script located at build folder of your installation directory.
Additional accessory scripts are available in the Accessories directory.
You may make these callable by creating a softlink to any location on your path (in this case, the user's bin directory).
ln -s /path/to/MetaSanity/build/MetaSanity.py ~/bin/MetaSanity
ln -s /path/to/MetaSanity/Accessories/* ~/bin/The conda installation does not include PSortB installed by default. It provides (most of) the dependencies needed for users who have it installed locally.
We provide a helper script psortb-install.sh, but it would need to be run using sudo, so we advise users to request help from their sysadmin prior to installation.
Users will also need to set the required environment variables that are listed at the bottom of the script.
MetaSanity v1.3.0 incorporates VirSorter2.2.3 into its pipeline, which provides output in a different format than in previous versions.