Greg Von Kuster

@bgruening The installation instructions for https://github.com/paolo-f/bcfind install the head of the git repo. For the tool_dependencies.xml recipe, should I use a "git clone..." followed by a "git checkout..." as the...

@nsoranzo Thanks, I'll go that route and use the current repo head as the commit hash.

@bgruening @nsoranzo This package is going to require a fairly complex installation recipe with many dependencies (e.g., PIL, tables, pandas, scikit-learn, progressbar-latest, numpy, scipy, mahotas, ujson) all installed into a...

@bgruening I've got the installation recipes with all dependencies basically done for bcfind. I noticed that your current tool outline at https://github.com/bgruening/galaxytools/blob/master/tools/image_processing/bcfind/bcfind.xml has set the bcfind dependency version to 1.3.18...

@bgruening ok, just to confirm, should it be "ed3ea2c29d"? Thanks!

@bgruening Need some insight on the tool(s) you are looking for here. The bcfind manual at http://bcfind.dinfo.unifi.it/guide.html sort of implies a suite of tools as: bcfind_make_substacks bcfind_cell_finder bcfind_measure_performance bcfind_supervised_semantic_deconvolution bcfind_merge_markers...

Thanks Bjorn, I’ll keep this on my list, but it will be a while. I’m currently buried with Galaxy consulting for 1 lab and I have an additional lab I’ll...

@abretaud This is the line of code in the local job runner that is blocking the Java call: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/local.py#L100. Commenting out the ```preexec_fn=os.setpgrp``` parameter will unblock the local job runner...

@tischi, it's great to see others interested in wrapping imagej2 tools for Galaxy! The current Galaxy tools were written almost 5 years ago, but they are still maintained. We recently...

This sounds great! The current tools also invoke commands headless from the command line - https://github.com/bgruening/galaxytools/blob/master/tools/image_processing/imagej2/imagej2_base_utils.py#L35. It's fantastic that you have been able to eliminate all Jython calls as this...