1. Installation

If you are a developer, you would want to install Sequana from source. There are lots of dependencies that require compilation and may be time consuming. We therefore recommend the Anaconda solution. Sequana is indeed available on bioconda. Note, however, that releases of Sequana are also available on Pypi so you could also use pip.

If you just want to test Sequana or Sequanix or one of the Sequana standalone, we have started to provide Singularity containers since version 0.5.2. This is a great solution for reproducibility as well. Containers are available on https://singularity-hub.org/collections/433/.

1.1. Overview of installation methods

We support 3 types of installations:

  1. Singularity. Strictly speaking, there is no compilation. This method is for testing and production. It downloads an image / container that is ready-to-use:

    singularity pull shub://sequana/sequana:master
    singularity shell sequana-sequana-master.img
    
  2. Bioconda. Sequana is available on conda/bioconda as a pre-compiled package:

    conda install sequana
    
  3. From source. If you prefer to install everything yourself, the source code is available on github (http://github.com/sequana/sequana) and releases are posted on Pypi:

    pip install sequana
    

These three methods are detailled hereafter.

1.3. From Pypi website (released source code)

If you do not want to use conda, we provide releases on the Python Package Index website (pip tool):

pip install sequana
pip install PyQt5

Warning

we do not support this methods but it should work. The main issues being that you will need to install the dependencies yourself. See hereafter for some of the tool used by the pipelines

1.4. From GitHub Source code

Finally, if you are a developer and wish to use the latest code, you can install sequana from source:

git clone git@github.com:sequana/sequana.git
cd sequana
python setup.py install

This should install most of the required dependencies. However, you may need to install more packages depending on the pipeline used. See hereafter.

1.5. Singularity

We provide Singularity images on https://singularity-hub.org/collections/433/ . They contain Sequana standalones and some of the pipelines dependencies as well as Sequanix. Note, however, that Sequanix relies on PyQt (graphical environment) and would work for Linux users only for the time being. The main reason being that under Mac and windows a virtualbox is used by Singularity preventing a X connection. This should be solved in the near future.

First, install singularity (http://singularity.lbl.gov/). Second, download a Sequana image. For instance, for the latest master version:

singularity pull shub://sequana/sequana:master

Do not interrupt the download (4-5Go). Once downloaded, you can use, for instance, the sequana_coverage executable:

singularity exec sequana-sequana-master.img sequana_coverage --help

or sequanix:

singularity exec sequana-sequana-master.img sequanix

Would you miss a dependency, just enter into the singularity container and install the missing dependencies. You will need writable permission:

sudo singularity shell -w sequana-sequana-master.img

Then, inside the container, install or fix the problem and type exit to save the container.

Note

method tested with success on Fedora 23, ubuntu and Centos 6.

See also

Notes for developers about Singularity especially to get specific vresions.

1.6. Notes about dependencies

When installing Sequana with conda and from the source, it should install all the Python dependencies and you should be ready to go to use the Sequana Python library.

However, note that most of the pipelines rely on extra dependencies that are not necesseraly Python-based. For instance bwa is in C, others may be in R or perl.

The list of requirements is available in the source code:

https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines.txt

and conda may be used to install those dependencies automatically:

conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines.txt

Otherwise you need to proceed to the installation of those dependencies by yourself.

Note

atropos is an alternative to cutadapt with additional options but same type of functionalties and arguments. We use version 1.0.23 and above though.

Note

the denovo_assembly pipelines uses Quast tool, which we ported to python 3.5 and was pulled on Quast official github page. This is not yet in bioconda but one can get it from the quast github (sept 2016). This is

to be installed manually by users (due to licensing restrictions)

Note

For GATK (variant caller), please go to https://software.broadinstitute.org/gatk/download/auth?package=GATK and download the file GenomeAnalysisTK-3.7.tar.bz2 ; then type:

gatk-register GenomeAnalysisTK-3.7.tar.bz2

1.7. Docker containers for Sequana

We do not provide Docker containers for each release but thanks to bioconda one can get some Docer containers. For example version 0.4.1 is available as explained here below. For full list please checkout https://quay.io/repository/biocontainers/sequana

1.7.1. Example: sequana_coverage

To pull a Sequana container (here version 0.4.1), use this type of command:

docker pull quay.io/biocontainers/sequana:0.4.1--py35_0

Checkout the quay.io website. After pulling the image above, you can use it as follows:

docker run -v $PWD:/home/default -it quay.io/biocontainers/sequana:0.4.1--py35_0

Warning

once in the docker shell, go to /home/default. Here, this directory is linked to your real directory where you type “docker run…” so what you modify here is directly reflected in your directory !

Assuming you have a BED file JB409847 in your directory, otherwise uncomment the commented line here below:

cd /home/default
export MPLBACKEND="agg"
# wget https://tinyurl.com/y9j69t3k -O JB409847.bed
sequana_coverage --input JB409847.bed
exit

Back on your local directory, you should now see a ./report directory with the results of the analysis.