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08-RunningOwnPrograms.md

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title Retrieving, compiling and running own programs
author CSC Training
date 2019-12
lang en

Installing Qiime2

$ python -V
$ python3 -V
$ wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
$ bash Miniconda2-latest-Linux-x86_64.sh
$ exit
$ conda update conda
$ conda install wget
$ wget https://data.qiime2.org/distro/core/qiime2-2019.10-py36-linux-conda.yml
$ conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-linux-conda.yml
$ conda activate qiime2-2019.10

Why Conda?

  • Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux.
    • Conda quickly installs, runs and updates packages and their dependencies.
    • You can set up totally separate environments to run different versions of software, while continuing to run your usual commands in your normal environment.
    • Miniconda is “mini” because by default, it does not include as many Python packages as Anaconda does. A minimum number of default packages uses less space on hard drives.
  • Miniconda in not installed by default on Linux.

Conda basics

  • To create/remove a new environment and install/remove software into it:
$ conda create -n env_name software [ software … ]
$ conda remove env_name
  • To use installed software in its environment:
$ conda activate env_name
  • To stop using software:
(env_name) $ conda deactivate
  • Enable/disable Conda base at startup:
$ conda config --set auto_activate_base true|false

Bioconda

  • Bioconda is a channel for the conda package manager specializing in bioinformatics software, see Bioconda web page for more information.
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda create -n aligners bwa bowtie
$ conda activate aligners
$ conda deactivate

Compiling from source code

  • If you are absolutely sure a ready-made executable does not exist, you need to compile the software yourself.
$ wget https://ftp.gnu.org/gnu/hello/hello-2.10.tar.gz
$ tar xzf hello-2.10.tar.gz
$ cd hello-2.10
$ ./configure --prefix=${HOME}/hello
$ make
$ make install
$ make clean
  • Development libraries required for compiling might be missing from default install. If that's the case those need to be installed first.
$ sudo apt install libc-dev