/nextseq_illumina

Scripts for automated FASTq file upload to basespace from Illumina NGS machines (e.g. NextSeq 2000)

Primary LanguageShell

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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

    2. 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:
      2. 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:
      3. ln -s ~/.local/bscmd ~/.local/bs && chmod +x ~/.local/bs*

    3. creating authentication token (just 1st time per server).
      4. 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
      5. 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:

    3. 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:

    4. 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