External MBEDTLS version mismatch with Julia but not with bash

Question

[marongiu.luigi]

Hello

I am running a shell script that launches blastx. From terminal it works but launching the script from Julia gives this error:

julia> x_blast = read(pipeline(`.../fetcher.sh`), String)
Critical: [blastx] External MBEDTLS version mismatch: 2.16.0 headers vs. 2.16.2 runtime

would you know what it is about?

[Ram]

Most commands that "work when run on the shell but don't work when a wrapper is added" probably stop working because they rely on one of the dot file settings. In your case, probably, there is a PATH variable that needs to be read in for the command to find the right version of a tool.

Try running the same command using bash --noprofile -c "<command>" and if that fails, you'll know that the problem is caused by a dotfile setting.

[marongiu.luigi]

I tried with

x_blast = read(pipeline(`bash --noprofile -c /home/gigiux/Downloads/h32/fetcher.sh`), String)
Critical: [blastx] External MBEDTLS version mismatch: 2.16.0 headers vs. 2.16.2 runtime

[Ram]

Try running the bash --noprofile command from the shell, not from within Julia. You're debugging a dot file related problem and trying to do that while maintaining a wrapper, which makes no sense. Please try and understand what you're doing before you try to do it.

[ATpoint]

is this correct .../?

[marongiu.luigi]

it is the short for the real path, which is a bit long.

[Ram]

I guess ... is aliased to ../../. That could be causing a problem too, but doesn't look like it.

[h.mon]

Do you set or modify any environment variable before running the script on the command line? Do you have to load something with module load xxx-yyy? What is the content of the fetch.sh script?

You can speed up a lot the process of getting help if you are more careful and detailed when asking questions.