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INSTALL.md

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LOREAN INSTALLATION

IMPORTANT

LoReAn uses GeneMark-ES as ab-initio software which needs a license key to run.

Therefore, IT IS MANDATORY TO download the 64 bit Linux version key for GeneMark-ES/ET v.4.48_3.60 website, un-gunzip the key and place it in the right location.

LoReAn using SINGULARITY.

We prefer SINGULARITY to DOCKER because root access is not required.

The best way to use LoReAn is by installing and running the software via SINGULARITY. We advice to use LoReAn via SINGULARITY because the pipeline uses a lot of software which maybe time take to install separately.

Here the required steps before using LoReAn:

1) PLACE THE GENEMARK-ES KEY AT THE RIGHT PLACE

The first step is to place the GeneMark key in the home directory of the user running SINGULARITY. In Ubuntu, the end result would be ~/.gm_key

cd Downloads
gunzip gm_key_64.gz
mv gm_key_64 ~/.gm_key

2) DOWNLOAD THE REQUIRED FILES/FOLDERS

In order to run LoReAn by Singularity exec command, you need to download and unzip these two files:

wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1ZzbbHXYGLGtScrpC3SmRGT0w2DWBNRaP' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1ZzbbHXYGLGtScrpC3SmRGT0w2DWBNRaP" -O ./config.augustus.tar.gz && rm -rf /tmp/cookies.txt && tar -zxvf config.augustus.tar.gz && rm config.augustus.tar.gz
wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1hEhzvyLDRTLPJM_f7pibq9E9X7ral5j0' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1hEhzvyLDRTLPJM_f7pibq9E9X7ral5j0" -O ./RepeatMasker.Libraries.tar.gz && rm -rf /tmp/cookies.txt && tar -zxvf RepeatMasker.Libraries.tar.gz && rm RepeatMasker.Libraries.tar.gz

The firts file is the configuration folder from Augustus software (see below <PATH_TO_AUGUSTUS_CONF_FOLDER>) while the second file is the Libraries folder of RepeatMasker software (see below <PATH_TO_LIBRARY_FOLDER>)

Next you can download and build the Syngularity image using:

singularity pull docker://lfaino/lorean:latest

3) CHECK THAT LOREAN WORKS

Now, check if LoReAn works by

singularity exec -B <PATH_TO_AUGUSTUS_CONF_FOLDER>:/opt/LoReAn/third_party/software/augustus/config/ -B 
<PATH_TO_LIBRARY_FOLDER>:/usr/local/RepeatMasker/Libraries/ <PATH_TO_LOREAN_IMAGE>/lorean_latest.sif lorean -h

At this point, you should see the options list. You can continue by testing lorean using the toy datasets located at LoReAn examples

LoReAn using Docker.

On Linux system, make sure that the user runnig docker is added as user in docker user group.

On Windows system, before installing Docker IT IS MANDATORY to allow symbolic links. PASA makes symbolic during the run. The eisiest way to run docker is via Docker Toolbox. During the installation, set the size of the disk image to about 30Gb. After the installation run Docker Quickstart Terminal and follow the instruction below

IMPORTANT

LoReAn uses GeneMark-ES as ab-initio software which needs a license key to run.

Therefore, IT IS MANDATORY TO download the 64 bit Linux version key for "GeneMark-ES / ET v.4.48" website (http://exon.gatech.edu/GeneMark/license_download.cgi) and follow the intruction for the key.

The first step is to place the GeneMark key in the home directory of the user running SINGULARITY. In Ubuntu, the end result would be ~/.gm_key

cd Downloads
gunzip gm_key_64.gz
mv gm_key_64 ~/.gm_key

The best way to use LoReAn is by installing and running the software by Docker We used Docker because the pipeline uses a lot of software which maybe difficult to install independently.

To install Docker, please refer to: https://docs.docker.com/engine/installation/

After Docker installation, you can download LoReAn by using:

docker run -it --rm -v <PATH_TO_AUGUSTUS_CONF_FOLDER>:/opt/LoReAn/third_party/software/augustus/config/  
-v $HOME:/home/lorean  -v $PWD:/data -u $(id -u ${USER}):$(id -g ${USER}) lfaino/lorean:latest lorean -h