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  • Interconnecting 2 to 3 shell scripts

    Hi All,
    I have 3 to 4 working shell scripts
    for SRA to FASTQ
    FASTQ to BAM
    BAM to BEDGRAPH
    can I write single shell script interconnecting these shell which are working individually fine . If so it is creating me several problem like I am writing fastq files to a temporary folder which is not able is recognize by second shell . If there any online links to these kind of problems I would appreciate help. What are kinds of issues to consider while merging several shell programs .

    Thanks in advance,
    Anusha.Ch

  • #2
    Yes, you can write a single shell script wich is contains only other shell scripts. You need to set the command line parameters to each script get a proper input files. For example:
    #!/bin/bash

    ./first.sh input.sra >/tmp/out.fastq
    ./second.sh /tmp/out.fastq >/tmp/out.bam

    Even better, if you use variables, because there is less chance to misstype. For example:
    FASTQ=/tmp/out.fastq
    ./fist.sh input.sh >$FASTQ
    ./second.sh $FASTQ ...

    Comment


    • #3
      If you want to conserve space and get something close to pipe-like functionality, you can use FIFO buffers:

      Code:
      $ mkfifo test.txt
      $ cat test.txt &
      [1] 21854
      $ echo -e "blah\nblah\nblah" > test.txt
      $ blah
      blah
      blah
      
      [1]+  Fertig                  cat test.txt

      Comment

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