while working through the SLAW documentation, I encountered an ambiguous passage in the Quick Start of the SLAW Documentation which I would like to comment:
docker run --rm -v INPUT_FOLDER:/input -v PATH_OUTPUT:/output zambonilab/slaw:latest
Here, it is unclear that INPUT_FOLDER and PATH_OUTPUT are variables that the user has to replace with the (absolute) path to the input- and output directories. I would recommend making them more evident by enclosing them in angle brackets and/or to mention the need for replacement explicetly in the text. It is my understanding that the docker container is directed to the lay user, which will copy&paste the command, get an error, become frustrated and stop using the program (e.g. see below).
$ docker run -v INPUT_FOLDER:/input -v PATH_OUTPUT:/output zambonilab/slaw:latest
2022-02-25|20:03:33|INFO: Total memory available: 3449 and 4 cores. The workflow will use 862 Mb by core on 4 cores. Traceback (most recent call last): File "/wrapper_docker.py", line 121, in <module> pol = exp.guess_polarity(INPUT) File "/pylcmsprocessing/model/experiment.py", line 109, in guess_polarity path_raw = all_path[0] IndexError: list index out of range
Apart from that, I think that SLAW is a great package and a much-appreciated alternative to the often cumbersome GUI tools.
Dear developers,
while working through the SLAW documentation, I encountered an ambiguous passage in the Quick Start of the SLAW Documentation which I would like to comment:
docker run --rm -v INPUT_FOLDER:/input -v PATH_OUTPUT:/output zambonilab/slaw:latestHere, it is unclear that INPUT_FOLDER and PATH_OUTPUT are variables that the user has to replace with the (absolute) path to the input- and output directories. I would recommend making them more evident by enclosing them in angle brackets and/or to mention the need for replacement explicetly in the text. It is my understanding that the docker container is directed to the lay user, which will copy&paste the command, get an error, become frustrated and stop using the program (e.g. see below).
$ docker run -v INPUT_FOLDER:/input -v PATH_OUTPUT:/output zambonilab/slaw:latest2022-02-25|20:03:33|INFO: Total memory available: 3449 and 4 cores. The workflow will use 862 Mb by core on 4 cores. Traceback (most recent call last): File "/wrapper_docker.py", line 121, in <module> pol = exp.guess_polarity(INPUT) File "/pylcmsprocessing/model/experiment.py", line 109, in guess_polarity path_raw = all_path[0] IndexError: list index out of rangeApart from that, I think that SLAW is a great package and a much-appreciated alternative to the often cumbersome GUI tools.
Kind regards,
Mitja Zdouc