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[scipion-users] Installing chimera plugin
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From: Lynn R. <lyn...@un...> - 2021-11-04 14:46:39
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Dear Scipion community, I have installed Scipion successfully and a number of plugins. However, the chimera plugin is giving problems. If I install it via the plugin manager, there are errors. I have tried uninstalling and reinstalling. If I install it with this command: $ scipion3 installp -p scipion-em-chimera Then it gives the following output: Scipion v3.0.9 - Eugenius Building scipion-em-chimera ... /home/ubuntu/.conda/envs/scipion3/bin/python -m pip install scipion-em-chimera==3.1.7 Collecting scipion-em-chimera==3.1.7 Using cached scipion_em_chimera-3.1.7-py3-none-any.whl (95 kB) Requirement already satisfied: scipion-em in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em-chimera==3.1.7) (3.0.13) Requirement already satisfied: tk-html-widgets in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em-chimera==3.1.7) (0.4.0) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (3.0.17) Requirement already satisfied: biopython==1.76 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (1.76) Requirement already satisfied: tifffile in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-chimera==3.1.7) (2021.11.2) Requirement already satisfied: numpy in ./.conda/envs/scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-chimera==3.1.7) (1.18.4) Requirement already satisfied: configparser<=5.0.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.0.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.1.3) Requirement already satisfied: mpi4py<=3.0.3 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.3) Requirement already satisfied: psutil<=5.8.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.8.0) Requirement already satisfied: matplotlib==3.2.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.2.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.25.1) Requirement already satisfied: pillow<=8.2.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (8.2.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.3.2) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.4) Requirement already satisfied: cycler>=0.10 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (0.11.0) Requirement already satisfied: python-dateutil>=2.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.8.2) Requirement already satisfied: future>=0.16.0 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (0.18.2) Requirement already satisfied: six>=1.5 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.16.0) Requirement already satisfied: chardet<5,>=3.0.2 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (4.0.0) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.26.7) Requirement already satisfied: idna<3,>=2.5 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.10) Requirement already satisfied: certifi>=2017.4.17 in ./.conda/envs/scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2021.10.8) Installing collected packages: scipion-em-chimera Successfully installed scipion-em-chimera-3.1.7 Done (0.54 seconds) Building chimerax-1.2.5 ... Skipping command: wget -nv -c -O /usr/local/bin/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /usr/local/bin/scipion/software/em/void.tgz.part /usr/local/bin/scipion/software/em/void.tgz All targets exist. cd /usr/local/bin/scipion/software/em mkdir /usr/local/bin/scipion/software/em/chimerax-1.2.5 Skipping command: tar -xf void.tgz -C chimerax-1.2.5 All targets exist. Skipping command: cd .. && python /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/getchimera.py 1.2.5 All targets exist. cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 cd .. && tar -xf ChimeraX-1.2.5.tar.gz cd /usr/local/bin/scipion/software/em/chimerax-1.2.5 mv ../chimerax-1.2.5-rc-2021.05.24/* . Skipping command: Link 'chimerax-1.2.5 -> chimerax-1.2.5' All targets exist. Done (6.28 seconds) Building scipionchimera-1.3 ... Skipping command: wget -nv -c -O /usr/local/bin/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /usr/local/bin/scipion/software/em/void.tgz.part /usr/local/bin/scipion/software/em/void.tgz All targets exist. cd /usr/local/bin/scipion/software/em mkdir /usr/local/bin/scipion/software/em/scipionchimera-1.3 Skipping command: tar -xf void.tgz -C scipionchimera-1.3 All targets exist. cd /usr/local/bin/scipion/software/em/scipionchimera-1.3 --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed- /bin/sh: 1: --nogui: not found Traceback (most recent call last): File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not built (after running ' --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed-') Error at main: target '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not built (after running ' --nogui --exit --cmd 'devel install /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion' && touch installed-') The trouble seems to start with "/bin/sh: 1: --nogui: not found". I also cannot use chimerax in the GUI. I would greatly appreciate your help on this issue. Kind regards, Lynn Radamaker |
