Use "/usr/bin/env bash" instead of "/bin/bash"

[unode]

Bug report

% nextflow run hello
N E X T F L O W  ~  version 20.04.1
Launching `nextflow-io/hello` [modest_lamarr] - revision: 1d43afc0ec [master]
WARN: The use of `echo` method is deprecated
executor >  local (4)
[a8/932405] process > sayHello (2) [100%] 1 of 1, failed: 1
WARN: Killing pending tasks (3)
Error executing process > 'sayHello (4)'

Caused by:
  Cannot run program "/bin/bash" (in directory "/tmp/work/7d/a941cf3b6cae277c641136cd0aee2d"): error=2, No such file or directory

Command executed:

  echo 'Hola world!'

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /tmp/work/7d/a941cf3b6cae277c641136cd0aee2d

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

The Tip actually runs as expected

% cd /tmp/work/fa/adc77db68ead7e6681d4e24f3df388
% bash .command.sh 
Bonjour world!

Expected behavior and actual behavior

On some systems /bin/bash doesn't exist. This causes failures at many levels since /bin/bash is hardcoded in many locations in nextflow's codebase, including the shebang of the nextflow-X.X.X.all release files.

The compatible alternative is to use /usr/bin/env bash or, if involving shebangs and multiple arguments, #!/usr/bin/env -S bash -ue. See also coreutils - env -S.

Environment

• Nextflow version: 20.04.1
• Java version: openjdk 11.0.6-internal 2020-01-14
• Operating system: Linux - NixOS 20.03
• Bash version: (use the command $SHELL --version)

% $SHELL --version
zsh 5.7.1 (x86_64-pc-linux-gnu)
% bash --version
GNU bash, version 4.4.23(1)-release (x86_64-unknown-linux-gnu)

[edmundmiller]

Same issue on Nixos 20.03 also.

#!/usr/bin/env bash

Works for me.

[unode]

Doing a quick search on /bin/bash shows that there are still other paths that might need to be corrected.

Pull request #1614 fixed only the nextflow launcher.

[pditommaso]

Well, the issue was automatically closed when merging the associated PR. Said that there's no plan to change the current usage of /bin/bash. This may have an impact on too many existing applications that's diffcult to assess.

Also, the proposed alternative suffers from the same issue. Try for example docker run busybox /usr/bin/env.

/bin/bash should be considered a requirement.

[unode]

Well, docker run busybox /bin/bash doesn't work either so that's a bit of an unfair comparison, but I understand the difficulty to assess other applications.

Would it be too risky to simply drop the full path whenever called from a script? i.e. /bin/bash args becoming bash args?
This is equivalent to using /usr/bin/env from shebangs.

I'm happy to provide a PR with the necessary changes to any existing reference to /bin/bash.

[pditommaso]

Not so unfair because busybox is used as base image for biocontainers to which /bin/bash is added and for NF support for containers is a paramount feature.

The only solution that I can see is to make the shell path configurable via config setting (env var or config file) which defaults to /bin/bash and the user can change as needed.

[edmundmiller]

Sorry this got closed automagically.

I agree that support for containers is a major feature and shouldn't be broken, and even if we convinced the biocontainers group to change, there are still tons of previous images that would still have /bin/bash.

I think making the shell path configurable is only only option also because of that. It's probably not a priority though because /bin/bash works on the majority of systems.

[edmundmiller]

Just came back to this as I was about to try to package up nextflow with nix. However, I just did ln -s /run/current-system/sw/bin/bash /bin/bash for any lost souls who find this.

[IllustratedMan-code]

Super quick flake for running under nixos:

{
    inputs = {};
    outputs = {self, nixpkgs, ...}:
    let
        system = "x86_64-linux";
        pkgs = import nixpkgs{inherit system;};
    in
    {
        devShells.${system}.default = with pkgs; (pkgs.buildFHSUserEnv {
            name = "nextflow";
            targetPkgs = pkgs: [pkgs.openjdk];
        }).env;
    };

}