My issue is with an ESP32 WROOM microcontroller. The IDE being used on the PI is version 1.8.19.
I have used it successfully to upload sketches to an Arduino Uno. I have a Raspberry Pi I am using for this setup. I am quite sure that what I did is kinda messy, but as it solved my issues, I thought it would be a good idea to share it.I am in the process of making a portable Arduino IDE system to allow access & upload of ino sketches to microcontrollers already installed in buildings on my property. I could solve both issues by a) installing simplejson in the galaxy virtualenv (I did so by adding "simplejson=3.13.2" in galaxy/requirements.txt and restarting galaxy) and b) adding the following line "("/mnt/extStorage/galaxy-app/lib")" just below "import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip" in the python wrapper ranger_wrapper.py). The xml wrapper (ranger_wrapper.xml) was calling a python wrapper ranger_wrapper.py) which was causing two issues: a) importError no module named simplejson, b) importError no module named galaxy. As an admin, I removed this faulty dependency from the admin panel, changed the link in tool_dependencies.xml to a valid one, and re-installed the missing dependency (actually, the peak ranger package) from the admin panel.
I will describe it here in case some people want to use this tool and face the same problem as I have.įirst of all, the link to download the tool in "tool_dependencies.xml" is obsolete. I was able to solve the issue in a very unorthodox way. By default, I dont have a $PYTHONPATH environment variable set up on my system (doing an echo prints nothing). I am using the most recent distribution of Galaxy with a virtual environment. I have read on forums that is is probably related to PYTHONPATH, but I don't exactly know how to fix it.
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip' Now I am facing a new problem when I try to run the tool Traceback (most recent call last):įile "/mnt/extStorage/shed_tools/toolshed.g2.bx.psu.edu/repos/modencode-dcc/peakranger/d6b1bb81fa6c/peakranger/ranger_wrapper.py", line 6, in I struggled a bit because the wrapper is old, the link to download the dependency was not working (in tool_dependencies.xml), and there were a lot of identation problems with the python wrapper called to execute the tool. I have recently installed PeakRanger from the Toolshed.
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