Installation#

Note

- CusProSe requires a python version >= 3.7

- CusProse has only been tested on Linux and MacOS systems.

External dependencies#

CusProSe relies on three external tools: hmmer, muscle and usearch. The first two can be easily installed from the following commands:

  • hmmer (tested with version 3.3)
sudo apt install hmmer
  • muscle (tested with version 3.8.1551)
sudo apt install muscle

For usearch, you first need to download it here: usearch (tested with version v10.0.240)

Next, you will have to rename it and make it accessible from anywhere in your system:

# rename to usearch
mv usearchXX.X.XXX_i86xxxx usearch

# make usearch executable
chmod +x usearch

# make usearch easily accessible
mkdir ~/bin
mv usearch ~/bin

Finally, execute the following command that will make usearch accessible to the system

echo -e "\n\n# Add usearch to PATH\nexport PATH=$PATH:~/bin" >> ~/.bashrc

Create an isolated environment#

Although not indispensable, this step is highly recommended (it will allow you to work on different projects avoiding potential conflicts between different versions of some python libraries).

Install virtualenv#

python3 -m pip install virtualenv

Create a virtual python3 environment#

virtualenv -p python3 my_env

Activate the created environment#

source my_env/bin/activate

Once activated, any python library you'll install using pip will be installed solely in this isolated environment.

Note

Every time you'll need to work with libraries installed in this environment (e.g. work on your project), you'll have to activate it.

Exit the activated environment#

Once you're done working on your project, simply type the following command to exit the environment.

deactivate

Download and install the latest release of CusProSe#

Click here for the latest release:

Uncompress the archive#

If you downloaded the .zip file:

unzip cusProSe-x.x.x.zip

If you downloaded the .tar.gz file:

tar xzvf cusProSe-x.x.x.tar.gz

Go to the cusProSe directory#

cd cusProSe-x.x.x/

You should have at this location the following architecture:

  .
  ├── docs
  ├── iterhmmbuild
  ├── lib
  ├── MANIFEST.in
  ├── mkdocs.yml
  ├── prosecda
  ├── README.md
  ├── scripts
  └── setup.py

Install CusProSe on your virtual environment#

Make sure that your virtual environment is activated and you are at the same level as the setup.py. Then type the following command: 

pip install .

Note

    If the installation successfully worked, then typing:
  • iterhmmbuild should display: 
    usage: iterhmmbuild [-h] -fa [FA] -protdb [PROTDB] [-name [NAME]] [-out [OUT]] [-id ID]
                    [-cov COV] [-cval CVAL] [-ival IVAL] [-acc ACC]
iterhmmbuild: error: the following arguments are required: -fa, -protdb
  • prosecda should display: 
    usage: prosecda [-h] -proteome [PROTEOME] -hmmdb [HMMDB] -rules [RULES] [-out [OUT]] 
                    [-cov COV] [-cevalue CVAL] [-ievalue IVAL] [-score SCORE] [-acc ACC]
                    [--nopdf]
prosecda: error: the following arguments are required: -proteome, -hmmdb, -rules
  • create_hmmdb should display: 
    usage: create_hmmdb [-h] -hmmdir [HMMDIR] [-dbname [DBNAME]] [-outdir [OUTDIR]]
create_hmmdb: error: the following arguments are required: -hmmdir
Note that all of those commands are accessible from anywhere in your system as long as your virtual environment is activated.