#Conda install package for python 2 how to#

The following will install Neptune locally into the source directory and will not require security privileges: neptune/INSTALL.shДЄlternatively, you may specify an install location, PREFIX, such as /usr/local/. Neptune will be installed using pip into its own Python virtual environment. If you cannot install the dependencies using the above script, the following dependencies must be manually installed, if necessary, by the user: The following operation will automatically install Neptune's dependencies and require security privileges (sudo) to install the dependencies: sudo neptune/install/debian_dependencies.sh However, this section should be compatible with any 64-bit Debian distribution. This is common to the Ubuntu operating system. This section assumes the user has the APT package manager. The following may check your Python version: python -version Note that Python 2.7 is provided with many major distributions of Linux. We provide more detailed instructions below.

Installing Neptune ( neptune/INSTALL.sh).

Installing dependencies (Ubuntu: sudo neptune/install/debian_dependencies.sh).

The direct Neptune installation involves the following: These instructions will likely require administrative privilages.

#Conda install package for python 2 how to#

The following instructions describe how to install Neptune directly. However, the benefit is that your system will be shielded from the Python 2.7 installation required by Neptune. It is important to note that this Neptune Bioconda environment will need to be activated in order to run the Neptune application. The current environment may be deactivated with the following: source deactivate This Neptune environment can be activated with the following: source activate neptune In this circumstance, we need to install Neptune within a Python 2.7 environment: conda create -name neptune python=2.7 neptune The follwing instructions assume you are using the Python 3.6 version of Miniconda. You can check if Neptune was installed correctly with the following: neptune -version After enabling Bioconda, Neptune may be installed as a Bioconda package with the following: conda install neptune The following instructions assume you are using Miniconda with Python 2.7, as described above. They must be added in this order so that priority is set correctly. You will need to add the following channels to conda. You can check if your Miniconda installation was successful with the following: conda -version After installation, you will then need to either open a new terminal or source your bashrc file in the current terminal for Miniconda to become available on the PATH: source ~/.bashrc You will likely want Miniconda to append the install location to your PATH and will need to select this option during the installation process. Miniconda may be installed with the follow instructions: wget Д¬hmod 755 Miniconda2-latest-Linux-x86_64.sh Miniconda (Python 2.7)Д«ioconda requires conda to be installed and we recommend using the Miniconda package. Installing the 'neptune' Bioconda package ( conda install neptune).The Bioconda-based Neptune installation involves the following: Otherwise, you will need to explicitly use Neptune within a conda environment. We recommend installing Miniconda using Python 2.7 64-bit Linux installer.

However, the choice of Miniconda only affects the Python version in root environment. There are two variants of the Miniconda installer: Python 2.7 and Python 3.6. We recommend installing conda with the Miniconda package. The simpliest way to install Neptune is using the Bioconda channel for the conda package management system. Neptune is known to be compatible with the SGE and Slurm schedulers. However, it is possible to run Neptune in parallel on a single machine without DRMAA. The installation and configuration of a DRMAA-compliant scheduler will require a significant understanding of Unix. Neptune achieves maximum parallelization when submitting jobs through a DRMAA-compliant cluster computing scheduler. Neptune may either be run on a single machine or a computing cluster.

Neptune may either be installed directly or as a Bioconda package. This installation guide assumes the use of the BASH Unix shell and a 64-bit Linux system.