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Prerequisites

All software requirements for the Raw ONT Reads Processing are managed and stored in a conda environment. However for Isoform Transcript Processing and Translated Isoform Feature Analysis, these tools need to be installed locally by the user. Even though IsoTV is a python-based pipeline, some of these external tools are only available for Linux based operating systems and are respectively marked below.

Installing Conda

Install conda as described at https://conda.io/docs/install/quick.html, or as below:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

See Source on how to install and activate the environment for use with the pipeline.

Note: Newer versions of conda may have have package conflicts errors when trying to activate the environment. If this is the case, try downgrading the conda version to 4.6.14.

conda install conda=4.6.14

Installing External Tools for Feature Analysis

IUPred2A (Disorder Region)

Install IUPred2A as described at https://iupred2a.elte.hu/download_new

InterProScan 5 (Protein Domain)

Install InterProScan as described at https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload, or as below:

mkdir my_interproscan
cd my_interproscan
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.46-81.0/interproscan-5.46-81.0-64-bit.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.46-81.0/interproscan-5.46-81.0-64-bit.tar.gz.md5

md5sum -c interproscan-5.46-81.0-64-bit.tar.gz.md5

tar -pxzf interproscan-5.46-81.0-64-bit.tar.gz

Note: May involves additional requirements (e.g. PANTHER).

cd data
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz.md5

md5sum -c panther-data-14.1.tar.gz.md5

tar -pxvzf panther-data-14.1.tar.gz

Brewery (Secondary Structure)

Install Brewery as described at https://github.com/mircare/Brewery/, or as below:

git clone https://github.com/mircare/Brewery/ --depth 1 && rm -rf Brewery/.git

Note: Involves additional requirements (e.g. HHblits, UniRef90). HHblits should already be part of environment.yaml.

wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/uniprot20_2016_02.tgz
tar -zxvf uniprot20_2016_02.tgz

Prosite Scan (PTMs)

Install Prosite Scan from ftp://ftp.expasy.org/databases/prosite/ps_scan/.

wget ftp://ftp.expasy.org/databases/prosite/ps_scan/ps_scan_linux_x86_elf.tar.gz
wget ftp://ftp.expasy.org/databases/prosite/prosite.dat

tar -xvf ps_scan_linux_x86_elf.tar.gz