curl command not executing via shell script in bash

Question

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.

Solution

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).

Comments

[steeldriver]

In particular, $(< foo) is a bashism; the POSIX equivalent would be $(cat foo) - so $token will likely be empty when executed in /bin/sh.

[danzel]

@Salvo Comunque ...and now it works? Which part did you modify?

[Salvo Comunque]

@danzel I modified script with #!/bin/bash and token=$(cat gdc-user-token.2018-06-26T14_36_13.548Z.txt) thank you ...