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This article mainly introduces how to install Cogent in Pacbio, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

The specific steps are as follows:

1. Install Anaconda, which can be found in our previous documentation for installing Iso-seq3.

two。 Press the dependency package of Cogent

Conda install-n anaCogent5.2 biopythonconda install-n anaCogent5.2-c http://conda.anaconda.org/cgat bx-pythonconda install-c http://conda.anaconda.org/timcera pulp

3. Install Cogent, the current version is v3.5

The latest version of cd git clone https://github.com/Magdoll/Cogent.gitcd Cogent# is v3.5git checkout tags/v3.5git submodule update-- init-- recursivecd Complete-Striped-Smith-Waterman-Library/srcmakeexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Cogent/Complete-Striped-Smith-Waterman-Library/srcexport PYTHONPATH=$PYTHONPATH:/Cogent/Complete-Striped-Smith-Waterman-Library/srccd. /.. / python setup.py buildpython setup.py install

4. Verify that the Cogent installation is successful

Run_mash.py-version

If you can output the version information of Cogent by executing this command, then the installation is successful

Thank you for reading this article carefully. I hope the article "how to install Cogent in Pacbio" shared by the editor will be helpful to everyone. At the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

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