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Reimplementation of RNAit RNAi primer selection tool

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RNAit

Reimplementation of RNAit RNAi primer selection tool

RNAit is a tool for selecting RNAi primers for Trypanosome genomes, originally implemented in Perl (see Redmond et al. (2003) RNAit: an automated web-based tool for the selection of RNAi targets in Trypanosoma brucei, Mol. Biochem. Parasitol.)

This is a reimplementation to replace the now offline original deployment

Setting up a development instance (MacOS)

bash 4 is required for helper scripts, whereas the MacOS default is 3.2, so grab a newer version with brew...

brew install bash

Create a conda environment, and add the RNAIT_ROOT variable to point to the location of the RNAit software....

conda create -n RNAit
mkdir -p ~/miniconda3/envs/RNAit/etc/conda/activate.d
mkdir -p ~/miniconda3/envs/RNAit/etc/conda/deactivate.d
echo '#!/bin/env bash' > ~/miniconda3/envs/RNAit/etc/conda/activate.d/vars.sh
echo "export RNAIT_ROOT=/path/to/RNAIT/" >>  ~/miniconda3/envs/RNAit/etc/conda/activate.d/vars.sh
echo '#!/bin/env bash' > ~/miniconda3/envs/RNAit/etc/conda/deactivate.d/vars.sh
echo "unset RNAIT_ROOT" >>  ~/miniconda3/envs/RNAit/etc/conda/deactivate.d/vars.sh
source activate RNAit

We need to install nginx,uwsgi,nodejs,biopython,primer3,primer3-py and blast from conda, and symlink the nginx config in place...

conda install nginx uwsgi nodejs biopython primer3 primer3-py blast pyyaml
mv $CONDA_PREFIX/etc/nginx/sites.d/default-site.conf $CONDA_PREFIX/etc/nginx/sites.d/default-site.conf.hiding
ln -s ${RNAIT_ROOT}/etc/nginx-site.conf $CONDA_PREFIX/etc/nginx/sites.d/

The node.js broken-link-checker is used for verifying HTML pages, while vnu (available via brew) is used for HTML syntax validation

npm install -g broken-link-checker
brew install vnu
brew install java

Syntax and link checking is carried out using bin/check_pages.sh. Ensure the correct path to the vnu installation is set in the script, since this will vary according to the version when installed with brew...

etc/uwsgi will need to be edited to set correct paths dependent upon the location of the RNAit directory

The nginx and uwsgi instances can be started and stopped using:

bin/start_servers.sh
bin/stop_servers.sh

UWSGI can be made to reload the python scripts when these are modified by touching the uwsgi/reload file.

Setting up a production instance

TODO: WriteMe!

Blast Databases

Blast databases are obtained where possible from CDS sequences from ensembl distributions. Each database has a 'short name' which is the blast database name and is the value passed through the 'database' form parameter.

When adding a database, it also needs to be added to the 'database' input field of htdocs/index.html, and it's short name to the params_check.database which is used for server-side paramater validation.

Details on the databases are as follows:

Species Short name Source file Source
Trypanosoma brucei TREU927 TbruceiTREU927 TriTrypDB-37_TbruceiTREU927_AnnotatedCDSs.fasta TryTrypDB Release 39
Trypanosoma brucei lister 427 TbruceiLister427 TriTrypDB-37_TbruceiLister427_AnnotatedCDSs.fasta TryTrypDB Release 39
Trypanosoma brucei gambiense DAL972 TbruceiGambienseDAL972 TriTrypDB-37_TbruceigambienseDAL972_AnnotatedCDSs.fasta TryTrypDB Release 39
Trypanosoma congolense IL3000 TcongolenseIL3000 TriTrypDB-37_TcongolenseIL3000_AnnotatedCDSs.fasta TryTrypDB Release 39

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