Differences between revisions 1 and 7 (spanning 6 versions)

Installing software

Contents

Installing software

Installing software or pipeline can be a difficult task to accomplish. Therefore we suggest all users to make the programs they installed available to all users whenever it is possible. In general programs/pipelines that should be available to all are installed in /tools folder. On this page will be described how to make tools available on our system for installation procedure of your specific program please refer to the instructions coming with that program.

Who can install software

In principle any users except students and guests should be able to install bioinfo tools in folders made for that purpose.

Test data

We do ask users to provide test data for all install software. This way it becomes easy to check whether a software works or not. It is also good to define default command to test a tool, see next section to know more about this.

Install binaries

Coming soon

Use easybuild

Coming later

Install miniconda/anaconda packages

Anaconda (or Conda) is a well known program for managing environments and packages. It is very popular inn bioinformatics as it allows users with little experience to easily install needed tools and all dependencies. It also makes it easy for users to load the specific environments they need without modifying their bashrc themselves.

On this server you will find 2 versions of miniconda installed, miniconda3 for python 3 and miniconda2 for python 2.7 environments.

Conda's users guide can be found here, https://docs.conda.io/projects/conda/en/latest/user-guide/index.html.

Load conda module and set needed for conda to work. Be aware that this process rebase you default python bin folder into conda base folder.

   1 module load miniconda3/4.8.2
   2 source $CONDA_INIT

   1 which python
   2 #/tools/software/bioinfo-tools/miniconda/miniconda3/bin/python
   3

You can see all available environments
To make it easy for all users to locate needed environments, use descriptive names when making new environments, eg. software-exact_version_number.

   1 conda info --envs
   2 # OR
   3 conda env list
   4 ## conda environments:
   5 ##
   6 #test                     /home/fhoma/.conda/envs/test
   7 #base                  *  /tools/software/bioinfo-tools/miniconda/miniconda3
   8

Activate an existing environment

   1 conda activate <environment_name>
   2 # For example, you can try
   3 conda activate base

Deactivate the current environment

   1 conda deactivate

Load 2 conda environments (we do not recommend doing this as it may lead to big confusions)
Nested environment

   1 conda activate --stack <env_name>

Create new conda environment, there are 2 ways of doing this
from scratch or from a YAML config file. The latter one will create the environment and install all listed software
You can also give a list of software and versions when installing from scratch
Replace <env_name>, with a descriptive name.

   1 # Create an environment with only default packages
   2 conda create --name <env_name>
   3 # You can be asked to confirm the location of the location of the envs folder
   4 # Use the command below to accept any question by default
   5 conda create --yes --name <env_name>
   6 
   7 # Make an environment with python 3.6
   8 conda create --yes --name <env_name> python=3.6
   9 
  10 # Create an environment from YAML file
  11 conda env create -f <environment.yml>

Remove an unused environment

   1 conda env remove --name <env_name>
   2 # OR
   3 conda remove --name <env_name> --all

https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf

Install R packages

Packages for R are installed within R, so to install R packages, you will first need to load the module R and run R.

   1 module load R
   2 R

Use the following R command to print where are the R libraries. Users libraries are installed in /tools/R_libs/3.6.1

   1 .libPaths()
   2 #[1] "/tools/R_libs/3.6.1"
   3 #[2] "/opt/ohpc/pub/libs/gnu8/R/3.6.1/lib64/R/library"

To see all available/installed packages

   1 .packages(all.available=T)

To install R packages and dependancies. Installation will automatically be done in a /tools/R_libs/3.6.1 if permissions allows it. If not you could be asked to create a private one.

   1 install.packages(c("<package1>", "<package2>,..."), dep=T)

To install BIOINFORMATICS R PACKAGES, we recommend to use "bioconductor" channels.

   1 library(BiocManager)
   2 BiocManager::install(c("<package1>", "<package2>",...))

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 Installing software or pipeline can be a difficult task to accomplish.
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+== Test data ==

We do ask users to provide test data for all install software. This way it becomes easy to check whether a software works or not.
It is also good to define default command to test a tool, see next section to know more about this.

== Install binaries ==

Coming soon

== Use easybuild ==

Coming later

== Install miniconda/anaconda packages ==

Anaconda (or Conda) is a well known program for managing environments and packages. It is very popular inn bioinformatics as it allows users with little experience to easily install needed tools and all dependencies. It also makes it easy for users to load the specific environments they need without modifying their '''bashrc''' themselves.

On this server you will find 2 versions of miniconda installed, miniconda3 for python 3 and miniconda2 for python 2.7 environments.

Conda's users guide can be found here, https://docs.conda.io/projects/conda/en/latest/user-guide/index.html.

'''
 * Load conda module and set needed for conda to work. Be aware that this process rebase you default python bin folder into conda base folder.
'''
{{{#!highlight bash
module load miniconda3/4.8.2
source $CONDA_INIT
}}}
{{{#!highlight bash
which python
#/tools/software/bioinfo-tools/miniconda/miniconda3/bin/python
}}}

'''
 * You can see all available environments
 * To make it easy for all users to locate needed environments, use descriptive names when making new environments, eg. software-exact_version_number.
'''
{{{#!highlight bash
conda info --envs
# OR
conda env list
## conda environments:
##
#test                     /home/fhoma/.conda/envs/test
#base                  *  /tools/software/bioinfo-tools/miniconda/miniconda3
}}}

'''
 * Activate an existing environment
'''
{{{#!highlight bash
conda activate <environment_name>
# For example, you can try
conda activate base
}}}

'''
 * Deactivate the current environment
'''
{{{#!highlight bash
conda deactivate
}}}

'''
 * Load 2 conda environments (we do not recommend doing this as it may lead to big confusions)
 * Nested environment
'''
{{{#!highlight bash
conda activate --stack <env_name>
}}}
'''
 * Create new conda environment, there are 2 ways of doing this
 * from scratch or from a YAML config file. The latter one will create the environment and install all listed software
 * You can also give a list of software and versions when installing from scratch
 * Replace <env_name>, with a descriptive name.
'''
{{{#!highlight bash
# Create an environment with only default packages
conda create --name <env_name>
# You can be asked to confirm the location of the location of the envs folder
# Use the command below to accept any question by default
conda create --yes --name <env_name>

# Make an environment with python 3.6
conda create --yes --name <env_name> python=3.6

# Create an environment from YAML file
conda env create -f <environment.yml>
}}}

'''
 * Remove an unused environment
'''
{{{#!highlight bash
conda env remove --name <env_name>
# OR
conda remove --name <env_name> --all
}}}

 * https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf
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 #[1] "/tools/R_libs/3.6.1"
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+{{{#!highlight R
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