unexpected EOF while looking for matching `"' bash while im trying to execute command outs-CodePudding

I dont know what is happening here. Im executing a script that contains the following line:

var="${comand} bash -c  \"export PATH=/local/Miniconda3/bin:$PATH >> ~/.bashrc; /local/Miniconda3/bin/python3 scripts/DNAscan.py ${var}\""

echo "${var}"
$var

The output of that line is:

sudo docker exec -it image bash -c "PATH=/local//Miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin >> ~/.bashrc; /local/Miniconda3/bin/python3 scripts/DNAscan.py -format fastq -in input_output/input/test_data.1.fq.gz -in2 input_output/input/test_data.2.fq.gz -reference hg38 -alignment -variantcalling -annotation -iobio -out input_output/output/ -BED"

Bur when I try to execute it from the script it gives me the following error:

>>: -c: line 1: unexpected EOF while looking for matching `"'
>>: -c: line 2: syntax error: unexpected end of file

What can I do to solve this ?

CodePudding user response：

You don't really want docker exec here at all. This is a debugging tool that you can use to inspect a running container; I'd use it the same way I'd use a language-specific debugger like Python's pdb.

If you want to run a one-off command like this, you can use docker run. For example,

docker run                         \
  --rm                             \ # clean up this container when done
  -v "$PWD/data:/app/input_output" \ # make local files available in the container
  my-image                         \ # image name to run
  scripts/DNAscan.py               \ # command to run
    -format fastq                  \
    -in input_output/input/test_data.1.fq.gz \
    -in2 input_output/input/test_data.2.fq.gz \
    -reference hg38                \
    -alignment                     \
    -variantcalling                \
    -annotation                    \
    -iobio                         \
    -out input_output/output/      \
    -BED

The command you show does tries to write a .bashrc file inside the container setting up $PATH. However, most paths that run Docker containers don't actually read the .bashrc file at all. In your image's Dockerfile, you can use the ENV directive to set $PATH.

ENV PATH=/local/Miniconda3/bin:$PATH

Now we've gotten rid of the bash -c wrapper entirely, which will resolve your quoting problem.

#!/bin/sh

docker run --rm -v "$PWD/data:/app/input_output" my-image "$@"

The "$@" syntax passes the wrapper script's arguments as the docker run command argument, preserving any spaces or other punctuation in the argument list.