dear chimerax developers, i think i have tracked down the problem (centos7): when i removed the ~/.cache/ChimeraX directory everything runs fine now. first i tried to remove only the lock .cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock but this file stays even when chimerax is closed. and is overwritten with a new timestamp when a new instance is started. i tested to start in parallel a global chimerax and my development instance and the "ts list" for both instances is correct. so i am not sure what messed up my chimerax cache. cheers, wolfgang On 01/05/2017 05:13 PM, Wolfgang Lugmayr wrote:
dear chimera developers,
i'm currently porting one of our chimera 1.x plugins called starmap to chimerax.
basic questions: 1. should the package be e.g. chimerax-starmap or just starmap? 2. is there a recommended way when i should upload to the toolshed repository?
my current problem: i use chimerax's python3.5 pip to install and remove my tests. my test package is called chimerax.starmapx (+.__init.py__)
i had a look at your toolshed and added test categories like follows to the metadata (installed version): Classifier: ChimeraX :: Bundle :: Volume data :: 1,1 :: chimerax.starmap :: chimerax.starmap :: Classifier: ChimeraX :: Tool :: StarMapX :: Volume data :: Run Rosetta refinements Classifier: ChimeraX :: Command :: apix :: Volume data :: Run Rosetta apix Requires-Dist: ChimeraX-Core (>=0.1) Requires-Dist: pyparsing
i also used "General" instead of "Volume data" for debugging.
i have overriden the BundleAPI get_class, start_tools, register_command similar to blastprotein.
unfortunatly my test plugin never shows up in chimerax (e.g. ts list) and the command "stm apix" is not registered.
i debugged the toolshed (standalone - not in chimerax) and if i print the contents of line 720 - end of_load_bundle_infos() i get ...using SteamVR]], ChimeraX-StarMap (installed) [version: 0.1.2] [api package: chimerax.starmap] [category: Volume data] [tool: StarMap [categories: Volume data] [synopsis: Run Rosetta refinements]] [command: apix [categories: Volume data] [synopsis: Run Rosetta refinements]], ChimeraX-Stringdb (installed) [version: 0.1]... and a little bit before ('checking', <InstalledDistribution 'ChimeraX-StarMap' 0.1.2 at '/projects/marlovits/lugmayr/workspace/ChimeraX/lib/python3.5/site-packages/ChimeraX_StarMap-0.1.2.dist-info'>)
do i miss something during the registration process?
cheers, wolfgang
--- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr@uke.de http://www.cssb-hamburg.de/
--
_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
-- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.lugmayr@uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING