rogalmic/vscode-bash-debug

Bash Debug Problem

Closed this issue · 5 comments

davidRFB commented

We have written the needed data into your clipboard because it was too large to send. Please paste. when I try to perform a debug of code

for i in *.pdb;
do
echo ${i::-3}
prepare_ligand4.py -l $i -A hydrogens
cp config.txt ${i::-4}"dock.txt"
sed -i 's/TOCHANGE/'${i::-4}'/g' ${i::-4}"dock.txt"
#vina --cpu 8 --config ${i::-4}"dock.txt"
done

and cannot launch program setting the 'outfiles' attribute might help appears

Then I add

#!/usr/bin/env node
for i in *.pdb;
do
echo ${i::-3}
prepare_ligand4.py -l $i -A hydrogens
cp config.txt ${i::-4}"dock.txt"
sed -i 's/TOCHANGE/'${i::-4}'/g' ${i::-4}"dock.txt"
#vina --cpu 8 --config ${i::-4}"dock.txt"
done

debug execute but give me this error

/home/david/Scripts/Docking/VINA/AutoVINA.sh:3
for i in *.pdb;
^

SyntaxError: Unexpected identifier
at new Script (vm.js:79:7)
at createScript (vm.js:251:10)
at Object.runInThisContext (vm.js:303:10)
at Module._compile (internal/modules/cjs/loader.js:656:28)
at Object.Module._extensions..js (internal/modules/cjs/loader.js:699:10)
at Module.load (internal/modules/cjs/loader.js:598:32)
at tryModuleLoad (internal/modules/cjs/loader.js:537:12)
at Function.Module._load (internal/modules/cjs/loader.js:529:3)
at Function.Module.runMain (internal/modules/cjs/loader.js:741:12)

CPUs | Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz (4 x 2700)
GPU Status | 2d_canvas: enabledflash_3d: enabledflash_stage3d: enabledflash_stage3d_baseline: enabledgpu_compositing: enabledmultiple_raster_threads: enabled_onoop_rasterization: disabled_offprotected_video_decode: unavailable_offrasterization: disabled_softwareskia_renderer: disabled_off_okvideo_decode: unavailable_offviz_display_compositor: enabled_onviz_hit_test_surface_layer: disabled_off_okwebgl: enabledwebgl2: enabled
Load (avg) | 4, 4, 3
Memory (System) | 15.53GB (0.97GB free)
Process Argv | AutoVINA.sh --no-sandbox
Screen Reader | no
VM

Extension Author (truncated) Version
shell-format fox 7.0.1
bash-extension-pack liz 0.0.4
bash-ide-vscode mad 1.8.0
python ms- 2020.3.71659
powershell ms- 2020.3.0
autodocstring njp 0.4.0
shellman Rem 4.4.0
bash-debug rog 0.3.7
shebang-snippets rpi 0.1.4
bash-beautify sha 0.1.1

Thank you for your time and consideration

rogalmic commented

Not sure what is the issue here, but please try using proper shebang for bash.

The error stack indicates that shell script is interpreted by nodejs...

davidRFB commented

using #!/bin/sh
this message appears
Selección_007

my launch.json
{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [

    {
        "type": "node",
        "request": "launch",
        "name": "Launch Program",
        "skipFiles": [
            "<node_internals>/**"
        ],
        "program": "${file}"
    }
]

}

rogalmic commented

Please notice, that you are using node debugger extension in launch.Json. You need to create bash config to debug shell script.

davidRFB commented

Hi.
thank you for your quick answer. I am new in vscode and I do not understand how to create this bash config. Any recommendation?