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      Script for automatic upload of FASTq files to BaseSpace server/-s

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DATE:  22.03.2022
VERSION: 1.0
CREATOR: T.J.SANKO
ADDRESS: Stellenbosch University, Tygerberg Campus,
       Francie van Zijl Drive, Cape Town, South Africa
CONTACT: tjsanko@sun.ac.za

1. Requirements
Script is design to work on any linux machine with bash/shell language. It was tested on CentOS7 and Ubuntu SMP 20.04.1.
Requires active BasespaceCLI program on the machine with



Installation of BasespaceCLI on linux machines:

1. download:
you might be required to use "sudo" infront and type the super user password (root permissions)

mkdir -p ~/.local
wget "https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" -O ~/.local/bscmd


2. adding alternative name and changing permissions to execute:
ln -s ~/.local/bscmd ~/.local/bs && chmod +x ~/.local/bs*


3. creating authentication token (just 1st time per server).
By default, the token is created for USA server when the website address is not given.
~/.local/bscmd auth



or with alias "usa"

~/.local/bscmd auth -c usa --api-server https://api.basespace.illumina.com



if you want to authenticate connection to the European (EUC1) server:
~/.locla/bscmd auth -c eu --api-server https://api.euc1.sh.basespace.illumina.com



!!! Option "-c" allows to add alias/name for the server. Allowed are names: "eu", "usa" or "us" (case insensitive).
Not using "-c" option sets the server address to default (USA server)



4. setup of aliases and PATHs for the program
echo 'alias bs=" ~/.local/bs"' >> ~/.bashrc
echo 'alias bscmd=" ~/.local/bscmd"' >> ~/.bashrc



and for the script:
echo 'export PATH=$PATH:'/path_to_script_bs_upload/' >> ~/.bash_profile



More on installation (eg. on Mac or Windows) is available on Illumina website:
https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview



2. Syntax:
bs_upload.sh [options]



eg.
bs_upload.sh -l run222.lst -s eu -p /path_to_fastq_files/ -t 20 -T 48h



or alternative
bs_upload.sh -l run222.lst -s eu -p /path_to_fastq_files/ -t 20 -P XXXXXXX

3. Options:
required:

    l         list with files (run & LIMS numbers) in format: "RUNXXX,K0YYYYY"

optional:

    s         server name [eu|us|usa] (default: USA)
    L         List all projects available"
    p         path to FASTq files (default: current location)
    t         number of threds to use (default: t=4)
    T         time frame to look for project ID in hours (default: 24h)
    P         project ID number (default: obtained from the server based on the time frame in -t parameter). 
              ! only 1st entry from the list will be used
    h         prints this help
    help      prints this help