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kantale / OpenBio.eu

An Open Collaborative Scientific Environment
BSD 3-Clause "New" or "Revised" License
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Argo: Script with tool installation commands is empty #249

Open kantale opened 2 years ago

kantale commented 2 years ago

When submitting a workflow. A directory is created /private/openbio/<NICE_ID> where all intermediate scripts and files are created. In there the scripts that contain the installation commands for the tools are empty:

 root@ubuntu-18-04-8bd9575-8tdtr:/private/openbio/dogtrf18# ls -l
total 32
-rwxr-xr-x 1 root root    0 Jan 13 10:38 Dockerfile
drwxr-xr-x 2 root root    6 Jan 13 10:38 dogtrf18
-rw-r--r-- 1 root root  603 Jan 13 10:38 dogtrf18.html
-rw-r--r-- 1 root root  453 Jan 13 10:39 dogtrf18.tgz
-rw-r--r-- 1 root root    0 Jan 13 10:38 dogtrf18_inputs.sh
-rwxr-xr-x 1 root root    0 Jan 13 10:38 install-tool-test1__1__1.sh   <-- THIS IS EMPTY !!!
-rw-r--r-- 1 root root   57 Jan 13 10:39 obc_current_token.sh
-rw-r--r-- 1 root root 3235 Jan 13 10:38 obc_functions.sh
-rw-r--r-- 1 root root   21 Jan 13 10:38 step__main_step__test1__1__1_VARS.sh
-rw-r--r-- 1 root root   21 Jan 13 10:39 step__main_step__test1__1__2_VARS.sh
-rw-r--r-- 1 root root   21 Jan 13 10:39 step__main_step__test1__1__3_VARS.sh
-rw-r--r-- 1 root root   30 Jan 13 10:38 test1__1__1_VARS.sh

This hinders a lot the debugging process. It would be nice to have the commands that install a tool. This is an example when trying to run this workflow: https://openbio.platform.science-hangar.eu/platform/w/test1/1

chazapis commented 1 year ago

Should be reevaluated after the new Argo converter.