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Salvo Comunque
Asked: 2018-06-27 15:33:53 +0800 CST

curl command not executing via shell script in bash

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I'm learning shell scripting! For the same I've tried downloading the TCGA genome data using curl on ubuntu (Ubuntu 16.04.3 LTS) terminal.

sh. content

#!/bin/sh

echo /0c8a6022-b770-4a83-bac3-b1526a16c89a/;

token=$(<gdc-user-token.2018-06-26T14_36_13.548Z.txt)

export ec=18; while [ $ec -ne 0 ]; do curl -C - -H "X-Auth-Token: $token" 'https://api.gdc.cancer.gov/slicing/view/0c8a6022-b770-4a83-bac3-b1526a16c89a?region=chr9:131270948-131270948' > STAD/chr9:131270948-131270948_C440.TCGA-BR-6453-01A-11D-1800-08.3_gdc_realn.bam; export ec=$?;done

If I run the sh script, downloaded file is empty, without any error message.

But if the run the command directly then it is working fine.

I will appreciate if anyone let me know the mistake I am doing in the script.

scripts command-line sh curl

1 Answers

  1. Best Answer

    You are probably not running the script in bash.

    /bin/sh is a symlink to /bin/dash, the default non-interactive shell in Ubuntu (since version 6.10). dash doesn't support the shortcut command $(<filename), so your token variable is empty.

    To execute the script with bash, change the shebang line to #!/bin/bash or explicitly invoke bash script.sh.

    Generally, if you want/need to use a specific shell, you should explicitly specify it in the shebang line. If you want your script to be portable, you can specify #!/bin/sh, but then you have to make sure your script is POSIX-compliant. For example, the POSIX-compliant equivalent of $(<filename) would be $(cat filename).

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