First time installation¶
$ conda install thapbi_pict
The availability of all the command line dependencies likely rules out using Windows.
Alternatively, since the software is on the Python Package Index (PyPI), the following command will install it along with its Python dependencies:
$ pip install thapbi_pict
However, in this case you will still need to install various external command
line tools like
hmmer, and others which are only used for some classifiers
swarm). If you have BioConda setup, use the following:
$ conda install --file requirements-ext.txt
If you are not using Conda, then on a typical Linux system most of the tools required will be available via the default distribution packages, although not always under the same package name.
On Debian (with the efforts of DebianMed), or Ubuntu Linux, try:
$ sudo apt-get install ncbi-blast+ cutadapt hmmer swarm trimmomatic
If you want to install the very latest unreleased code, you must download the
source code from the repository on GitHub - see the
for more details.
Once installed, you should be able to run the tool using:
This should automatically find the installed copy of the Python code. Use
thapbi_pict -v to report the version, or
thapbi_pict -h for help.
If you installed via conda, this should work:
$ conda update thapbi-pict
If you installed via pip, this should work:
$ pip install --upgrade thapbi-pict
Either way, you can check the installed tool version using:
$ thapbi_pict -v