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From: Christopher B. <chr...@gm...> - 2022-08-17 00:27:49
|
Hi Hong,
Your solution worked. I incorrectly edited my config file, many thanks!
~C
On Tue, 16 Aug 2022 at 13:31, Christopher Borsa <chr...@gm...>
wrote:
> Hi Hong,
>
> Thank you for your help, setting CONDA_ACTIVATION_CMD didn't do the trick.
> As I'm running Centos7, this might perhaps be a compiler/OpenGL issue.
>
> Many thanks,
>
> Christopher
>
> On Tue, 16 Aug 2022 at 12:46, HONG ZHAN via scipion-users <
> sci...@li...> wrote:
>
>> Hi Christopher,
>>
>> I think you that you might need to add this line in the first line after
>> [PLUGINS] in the scipion configuration (scipion.conf) file if not added
>> yet, I have the same issue before:
>>
>> CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda
>> shell.bash hook)”.
>>
>> Hope it is the same as my issue before…
>>
>> Best,
>> Hong
>>
>>
>>
>> > On Aug 16, 2022, at 11:39 AM, Christopher Borsa <
>> chr...@gm...> wrote:
>> >
>> > After downloading the installing the eman-tomo dev package, I receive
>> the following error message pasted below. I'm not sure if this is in fact a
>> conda issue or to do with OpenGL. Can someone shed some light on this?
>> >
>> > ~Christopher
>> >
>> > CommandNotFoundError: Your shell has not been properly configured to
>> use 'conda activate'.
>> > To initialize your shell, run
>> >
>> > $ conda init <SHELL_NAME>
>> >
>> > Currently supported shells are:
>> > - bash
>> > - fish
>> > - tcsh
>> > - xonsh
>> > - zsh
>> > - powershell
>> >
>> > See 'conda init --help' for more information and options.
>> >
>> > IMPORTANT: You may need to close and restart your shell after running
>> 'conda init'.
>> >
>> >
>> >
>> >
>> > --------------------------------------------
>> >
>> > Sometimes installation fails due to missing dependencies:
>> >
>> >
>> > - OpenGL::OpenGL or similar does not exists --> sudo apt-get install
>> libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils
>> mesa-common-dev libglu1-mesa libglu1-mesa-dev
>> >
>> >
>> > --------------------------------------------
>> >
>> > Traceback (most recent call last):
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
>> line 474, in <module>
>> > main()
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
>> line 297, in main
>> > installPluginMethods()
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
>> line 216, in installPluginMethods
>> > plugin.installBin({'args': ['-j', numberProcessor]})
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
>> line 166, in installBin
>> > environment.execute()
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 748, in execute
>> > self._executeTargets(targetList)
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 690, in _executeTargets
>> > tgt.execute()
>> > File
>> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
>> line 221, in execute
>> > command.execute()
>> > File
>> "/home/cryoEM_staff/.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
>> '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
>> not built (after running 'conda create -y -n emantomo-2.91_211111 --file
>> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
>> && conda activate emantomo-2.91_211111 && cd eman-build && cmake
>> ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
>> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
>> exit 1; } && make -j 1 && make install')
>> > Error at main: target
>> '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
>> not built (after running 'conda create -y -n emantomo-2.91_211111 --file
>> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
>> && conda activate emantomo-2.91_211111 && cd eman-build && cmake
>> ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
>> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
>> exit 1; } && make -j 1 && make install')
>> > _______________________________________________
>> > scipion-users mailing list
>> > sci...@li...
>> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
|
|
From: Christopher B. <chr...@gm...> - 2022-08-16 17:31:48
|
Hi Hong,
Thank you for your help, setting CONDA_ACTIVATION_CMD didn't do the trick.
As I'm running Centos7, this might perhaps be a compiler/OpenGL issue.
Many thanks,
Christopher
On Tue, 16 Aug 2022 at 12:46, HONG ZHAN via scipion-users <
sci...@li...> wrote:
> Hi Christopher,
>
> I think you that you might need to add this line in the first line after
> [PLUGINS] in the scipion configuration (scipion.conf) file if not added
> yet, I have the same issue before:
>
> CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda
> shell.bash hook)”.
>
> Hope it is the same as my issue before…
>
> Best,
> Hong
>
>
>
> > On Aug 16, 2022, at 11:39 AM, Christopher Borsa <
> chr...@gm...> wrote:
> >
> > After downloading the installing the eman-tomo dev package, I receive
> the following error message pasted below. I'm not sure if this is in fact a
> conda issue or to do with OpenGL. Can someone shed some light on this?
> >
> > ~Christopher
> >
> > CommandNotFoundError: Your shell has not been properly configured to use
> 'conda activate'.
> > To initialize your shell, run
> >
> > $ conda init <SHELL_NAME>
> >
> > Currently supported shells are:
> > - bash
> > - fish
> > - tcsh
> > - xonsh
> > - zsh
> > - powershell
> >
> > See 'conda init --help' for more information and options.
> >
> > IMPORTANT: You may need to close and restart your shell after running
> 'conda init'.
> >
> >
> >
> >
> > --------------------------------------------
> >
> > Sometimes installation fails due to missing dependencies:
> >
> >
> > - OpenGL::OpenGL or similar does not exists --> sudo apt-get install
> libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils
> mesa-common-dev libglu1-mesa libglu1-mesa-dev
> >
> >
> > --------------------------------------------
> >
> > Traceback (most recent call last):
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 474, in <module>
> > main()
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 297, in main
> > installPluginMethods()
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
> line 216, in installPluginMethods
> > plugin.installBin({'args': ['-j', numberProcessor]})
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
> line 166, in installBin
> > environment.execute()
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 748, in execute
> > self._executeTargets(targetList)
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 690, in _executeTargets
> > tgt.execute()
> > File
> "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 221, in execute
> > command.execute()
> > File
> "/home/cryoEM_staff/.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
> '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
> not built (after running 'conda create -y -n emantomo-2.91_211111 --file
> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
> && conda activate emantomo-2.91_211111 && cd eman-build && cmake
> ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
> exit 1; } && make -j 1 && make install')
> > Error at main: target
> '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
> not built (after running 'conda create -y -n emantomo-2.91_211111 --file
> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
> && conda activate emantomo-2.91_211111 && cd eman-build && cmake
> ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
> /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
> exit 1; } && make -j 1 && make install')
> > _______________________________________________
> > scipion-users mailing list
> > sci...@li...
> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: HONG Z. <hz...@wi...> - 2022-08-16 16:45:46
|
Hi Christopher,
I think you that you might need to add this line in the first line after [PLUGINS] in the scipion configuration (scipion.conf) file if not added yet, I have the same issue before:
CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)”.
Hope it is the same as my issue before…
Best,
Hong
> On Aug 16, 2022, at 11:39 AM, Christopher Borsa <chr...@gm...> wrote:
>
> After downloading the installing the eman-tomo dev package, I receive the following error message pasted below. I'm not sure if this is in fact a conda issue or to do with OpenGL. Can someone shed some light on this?
>
> ~Christopher
>
> CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
> To initialize your shell, run
>
> $ conda init <SHELL_NAME>
>
> Currently supported shells are:
> - bash
> - fish
> - tcsh
> - xonsh
> - zsh
> - powershell
>
> See 'conda init --help' for more information and options.
>
> IMPORTANT: You may need to close and restart your shell after running 'conda init'.
>
>
>
>
> --------------------------------------------
>
> Sometimes installation fails due to missing dependencies:
>
>
> - OpenGL::OpenGL or similar does not exists --> sudo apt-get install libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils mesa-common-dev libglu1-mesa libglu1-mesa-dev
>
>
> --------------------------------------------
>
> Traceback (most recent call last):
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 474, in <module>
> main()
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main
> installPluginMethods()
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 216, in installPluginMethods
> plugin.installBin({'args': ['-j', numberProcessor]})
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
> environment.execute()
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
> self._executeTargets(targetList)
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
> tgt.execute()
> File "/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
> command.execute()
> File "/home/cryoEM_staff/.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 '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o' not built (after running 'conda create -y -n emantomo-2.91_211111 --file /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt && conda activate emantomo-2.91_211111 && cd eman-build && cmake ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies; exit 1; } && make -j 1 && make install')
> Error at main: target '/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o' not built (after running 'conda create -y -n emantomo-2.91_211111 --file /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt && conda activate emantomo-2.91_211111 && cd eman-build && cmake ../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat /home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies; exit 1; } && make -j 1 && make install')
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Christopher B. <chr...@gm...> - 2022-08-16 16:39:49
|
After downloading the installing the eman-tomo dev package, I receive the
following error message pasted below. I'm not sure if this is in fact a
conda issue or to do with OpenGL. Can someone shed some light on this?
~Christopher
CommandNotFoundError: Your shell has not been properly configured to use
'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running
'conda init'.
--------------------------------------------
Sometimes installation fails due to missing dependencies:
- OpenGL::OpenGL or similar does not exists --> sudo apt-get install
libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils
mesa-common-dev libglu1-mesa libglu1-mesa-dev
--------------------------------------------
Traceback (most recent call last):
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
line 474, in <module>
main()
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
line 297, in main
installPluginMethods()
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
line 216, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
line 166, in installBin
environment.execute()
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 748, in execute
self._executeTargets(targetList)
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 690, in _executeTargets
tgt.execute()
File
"/home/cryoEM_staff/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
line 221, in execute
command.execute()
File
"/home/cryoEM_staff/.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
'/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
not built (after running 'conda create -y -n emantomo-2.91_211111 --file
/home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
&& conda activate emantomo-2.91_211111 && cd eman-build && cmake
../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
/home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
exit 1; } && make -j 1 && make install')
Error at main: target
'/home/cryoEM_staff/software/scipion/software/em/eman-2.91_211111/eman-build/libpyEM/CMakeFiles/pyPolarData2.dir/libpyPolarData2.cpp.o'
not built (after running 'conda create -y -n emantomo-2.91_211111 --file
/home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Conda_EmanCB.txt
&& conda activate emantomo-2.91_211111 && cd eman-build && cmake
../eman-source/ -DENABLE_OPTIMIZE_MACHINE=ON || { cat
/home/cryoEM_staff/software/scipion/software/em/scipion-em-emantomo/emantomo/requirements/Missing_Dependencies;
exit 1; } && make -j 1 && make install')
|
|
From: Pablo C. <pc...@cn...> - 2022-08-04 06:33:33
|
Thanks for confirming it worked!
All the best, Pablo.
On 3/8/22 23:37, Christopher Borsa wrote:
> Hi Pablo,
>
> Enforcing scipy==1.8.1 with scipion3 pip worked. I knew doing
> something such as your recommendation would fix this, that or wait for
> the next release. Many thanks!
>
> ~Christopher
>
>
> On Wed, 3 Aug 2022 at 04:10, Pablo Conesa <pc...@cn...> wrote:
>
> This should be fixed now in fresh new installations.
>
> On 3/8/22 8:50, Pablo Conesa wrote:
>>
>> Hi Cristopher, all. Yes that is a consequence of a nasty third
>> party updates that are causing this conflict. We will fix this
>> asap (we are on it)
>>
>>
>> I think this may work. Before installing xmipp run this:
>>
>> scipion3 run pip install scipy==1.8.1
>>
>>
>> On 2/8/22 18:41, Christopher Borsa wrote:
>>> I am attempting to run Scipion3 on a Centos7 workstation.
>>> Scipion3 installs cleanly, but upon installing xmipp I get the
>>> following error:
>>>
>>> pkg_resources.ContextualVersionConflict: (numpy 1.23.1
>>> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
>>> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>>> Error at main: (numpy 1.23.1
>>> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
>>> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>>>
>>> I have tried uninstalling/reinstalling numpy, scipy, and
>>> scipion-pyworkflow, but pip cannot find a dependency solution.
>>> (I can successfully install xmipp2 from the Scipion3 GUI)
>>>
>>> How should I go about trying to troubleshoot this?
>>>
>>> Kind regards,
>>>
>>> Christopher
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> --
>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Christopher B. <chr...@gm...> - 2022-08-03 21:37:39
|
Hi Pablo,
Enforcing scipy==1.8.1 with scipion3 pip worked. I knew doing something
such as your recommendation would fix this, that or wait for the next
release. Many thanks!
~Christopher
On Wed, 3 Aug 2022 at 04:10, Pablo Conesa <pc...@cn...> wrote:
> This should be fixed now in fresh new installations.
> On 3/8/22 8:50, Pablo Conesa wrote:
>
> Hi Cristopher, all. Yes that is a consequence of a nasty third party
> updates that are causing this conflict. We will fix this asap (we are on it)
>
>
> I think this may work. Before installing xmipp run this:
>
> scipion3 run pip install scipy==1.8.1
>
>
> On 2/8/22 18:41, Christopher Borsa wrote:
>
> I am attempting to run Scipion3 on a Centos7 workstation. Scipion3
> installs cleanly, but upon installing xmipp I get the following error:
>
> pkg_resources.ContextualVersionConflict: (numpy 1.23.1
> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
> Error at main: (numpy 1.23.1
> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>
> I have tried uninstalling/reinstalling numpy, scipy, and
> scipion-pyworkflow, but pip cannot find a dependency solution. (I can
> successfully install xmipp2 from the Scipion3 GUI)
>
> How should I go about trying to troubleshoot this?
>
> Kind regards,
>
> Christopher
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Pablo C. <pc...@cn...> - 2022-08-03 08:09:49
|
This should be fixed now in fresh new installations.
On 3/8/22 8:50, Pablo Conesa wrote:
>
> Hi Cristopher, all. Yes that is a consequence of a nasty third party
> updates that are causing this conflict. We will fix this asap (we are
> on it)
>
>
> I think this may work. Before installing xmipp run this:
>
> scipion3 run pip install scipy==1.8.1
>
>
> On 2/8/22 18:41, Christopher Borsa wrote:
>> I am attempting to run Scipion3 on a Centos7 workstation. Scipion3
>> installs cleanly, but upon installing xmipp I get the following error:
>>
>> pkg_resources.ContextualVersionConflict: (numpy 1.23.1
>> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
>> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>> Error at main: (numpy 1.23.1
>> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
>> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>>
>> I have tried uninstalling/reinstalling numpy, scipy, and
>> scipion-pyworkflow, but pip cannot find a dependency solution. (I can
>> successfully install xmipp2 from the Scipion3 GUI)
>>
>> How should I go about trying to troubleshoot this?
>>
>> Kind regards,
>>
>> Christopher
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2022-08-03 06:50:49
|
Hi Cristopher, all. Yes that is a consequence of a nasty third party
updates that are causing this conflict. We will fix this asap (we are on it)
I think this may work. Before installing xmipp run this:
scipion3 run pip install scipy==1.8.1
On 2/8/22 18:41, Christopher Borsa wrote:
> I am attempting to run Scipion3 on a Centos7 workstation. Scipion3
> installs cleanly, but upon installing xmipp I get the following error:
>
> pkg_resources.ContextualVersionConflict: (numpy 1.23.1
> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
> Error at main: (numpy 1.23.1
> (/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
> Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
>
> I have tried uninstalling/reinstalling numpy, scipy, and
> scipion-pyworkflow, but pip cannot find a dependency solution. (I can
> successfully install xmipp2 from the Scipion3 GUI)
>
> How should I go about trying to troubleshoot this?
>
> Kind regards,
>
> Christopher
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Christopher B. <chr...@gm...> - 2022-08-02 16:42:08
|
I am attempting to run Scipion3 on a Centos7 workstation. Scipion3 installs
cleanly, but upon installing xmipp I get the following error:
pkg_resources.ContextualVersionConflict: (numpy 1.23.1
(/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
Error at main: (numpy 1.23.1
(/home/scipion_user/.conda/envs/scipion3/lib/python3.8/site-packages),
Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
I have tried uninstalling/reinstalling numpy, scipy, and
scipion-pyworkflow, but pip cannot find a dependency solution. (I can
successfully install xmipp2 from the Scipion3 GUI)
How should I go about trying to troubleshoot this?
Kind regards,
Christopher
|
|
From: Pablo C. <pc...@cn...> - 2022-07-26 08:00:10
|
Hi Hong!, please join our slack channel here: https://join.slack.com/t/scipion/shared_invite/zt-1c9o7avlc-1Jw~zLBvS7eLF2xP7VbXVA On 15/7/22 21:13, HONG ZHAN via scipion-users wrote: > Dear all, > 1) Analyze Result causes error in Tomosegment annotation step. > I am following the youtube tutorial and the online documentation: > https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV_pySeg_workflow.html. > > After the annotate segmented membrane job is done, I clicked on > Analyze Results, it showed this error in the terminal. But I can open > by right click on the output in the Summary. I think this error is not > an issue, or am I wrong? > > 2)It might be new, what is the value for vesicle packaging size? I > assume it would be a value for parallelization job? Should I put 1? > > > Super thanks! > > Hong > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Pablo C. <pc...@cn...> - 2022-07-26 07:59:18
|
Dear Hong, I'll invite you to our slack channel for betatesters, you'll get better support there for functionality that is not yet released. On 15/7/22 21:13, HONG ZHAN via scipion-users wrote: > Dear all, > 1) Analyze Result causes error in Tomosegment annotation step. > I am following the youtube tutorial and the online documentation: > https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV_pySeg_workflow.html. > > After the annotate segmented membrane job is done, I clicked on > Analyze Results, it showed this error in the terminal. But I can open > by right click on the output in the Summary. I think this error is not > an issue, or am I wrong? > > 2)It might be new, what is the value for vesicle packaging size? I > assume it would be a value for parallelization job? Should I put 1? > > > Super thanks! > > Hong > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: HONG Z. <hz...@wi...> - 2022-07-15 19:13:49
|
Dear all, 1) Analyze Result causes error in Tomosegment annotation step. I am following the youtube tutorial and the online documentation: https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV_pySeg_workflow.html. After the annotate segmented membrane job is done, I clicked on Analyze Results, it showed this error in the terminal. But I can open by right click on the output in the Summary. I think this error is not an issue, or am I wrong? 2)It might be new, what is the value for vesicle packaging size? I assume it would be a value for parallelization job? Should I put 1? Super thanks! Hong |
|
From: Alberto G. M. <alb...@cn...> - 2022-07-15 08:33:06
|
Dear all, The XMIPP team has released the new version of Xmipp. Please welcome to *Xmipp 3.22.7-Helios. *For this version we have updated 195 files; the main new features are these*.* <https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md>**Feel free toinstall it <https://github.com/I2PC/xmipp#standalone-installation>, test it, report any problems <https://github.com/I2PC/xmipp/issues> if they arise and above all enjoy it! You can update *scipion-em-xmipp* with the plugin manager or with/.///scipion3 installp -p scipion-em-xmipp/ Xmipp-Team |
|
From: HONG Z. <hz...@wi...> - 2022-07-13 14:53:12
|
Dear Wolfgang and all,
Apparently, my PYTHON path was messed up with pytom... And all my plugins are installed in the wrong directory... Now I fixed all. I am glad not to rebuild system...
Thank you so much for the help and have a great day !
A+,
Hong
________________________________
From: Lugmayr, Wolfgang <w.l...@uk...>
Sent: Wednesday, July 13, 2022 9:07 AM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] emantomo plugin install
Dear Hong,
maybe it was not so clear, but the conda activation is in the PLUGINS section below the PYWORKFLOW in the config file.
In our case:
:
[PLUGINS]
CONDA_ACTIVATION_CMD = source /beegfs/cssb/software/em/scipion/3.0/miniconda/etc/profile.d/conda.sh
EM_ROOT = software/em
:
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
:
Cheers,
Wolfgang
________________________________
From: "Mailing list for Scipion users" <sci...@li...>
To: "Mailing list for Scipion users" <sci...@li...>
Cc: "HONG ZHAN" <hz...@wi...>
Sent: Wednesday, 13 July, 2022 15:14:35
Subject: [EXT] Re: [scipion-users] emantomo plugin install
Thanks Grigory and David,
I tried also adding the this line in scipion.conf, however the issue persisted. I also have installed eman2.91 before, it might miss things up. I will check my envs and if not, i will rebuild my system clean.
Pesyg seems having same issue…
Thank you so much for the reply.
Bien cordialement,
Hong
On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...> wrote:
Dear Hong,
It seems Scipion is not able to find the location of conda in your system, which is required to execute the programs integrated in emantomo.
The easiest way to solve this issue is to add a new variable to the Scipion config file. This file should be located in path/to/your/scipion/config/scipion.conf
The variable you will need is the following one (after the [PYWORKFLOW] section inside the file should be fine): CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)".
Best,
David
On 12/7/22 20:43, HONG ZHAN via scipion-users wrote:
Hi all,
I am trying to install emantomo plugin, however, it showed error message below, does anyone have idea how to solve this error?
Super thanks!
Hong
--------------------
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Traceback (most recent call last):
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
self._run()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
resultFiles = self._runFunc()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
return self._func(*self._args)
File "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", line 135, in preprocess
self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), tomoFile, tomo.getSamplingRate()),
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1454, in runJob
self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
process.runJob(log, programName, params,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
return runCommand(command, env, cwd)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' conda activate emantomo-2.91_211111 && e2proc3d.py Runs/000002_ProtImportTomograms/extra/overview_wbp.em /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc --apix=5.000000' returned non-zero exit status 1.
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: HONG Z. <hz...@wi...> - 2022-07-13 14:51:41
|
Dear Hironori, I did find my issue... I defined my PYTHON path for pytom... it made scipion confused... And all my plugins are installed in the wrong directory... Now I fixed all. Thank you so much for the help:D A+, Hong ________________________________ From: 稲葉弘哲 <hi...@me...> Sent: Wednesday, July 13, 2022 8:37 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] emantomo plugin install Dear Hong As David mentioned, adding "CONDA_ACTIVATION_CMD" to the config was necessary for EMAN and Pyseg installation when I installed them. In my case, "CONDA_ACTIVATION_CMD = . /usr/local/miniconda/etc/profile.d/conda.sh" worked. See also Topaz integration in https://github.com/scipion-em/scipion-em-topaz Best, Hironori Hironori Inaba Ph.d. Department of Histology and Cell Biology, Graduate School of Medicine, Mie University, Japan e-mail: hi...@me...<mailto:hi...@me...> 2022年7月13日(水) 22:16 HONG ZHAN via scipion-users <sci...@li...<mailto:sci...@li...>>: Thanks Grigory and David, I tried also adding the this line in scipion.conf, however the issue persisted. I also have installed eman2.91 before, it might miss things up. I will check my envs and if not, i will rebuild my system clean. Pesyg seems having same issue… Thank you so much for the reply. Bien cordialement, Hong On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...<mailto:dhe...@cn...>> wrote: Dear Hong, It seems Scipion is not able to find the location of conda in your system, which is required to execute the programs integrated in emantomo. The easiest way to solve this issue is to add a new variable to the Scipion config file. This file should be located in path/to/your/scipion/config/scipion.conf The variable you will need is the following one (after the [PYWORKFLOW] section inside the file should be fine): CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)". Best, David On 12/7/22 20:43, HONG ZHAN via scipion-users wrote: Hi all, I am trying to install emantomo plugin, however, it showed error message below, does anyone have idea how to solve this error? Super thanks! Hong -------------------- CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run $ conda init <SHELL_NAME> Currently supported shells are: - bash - fish - tcsh - xonsh - zsh - powershell See 'conda init --help' for more information and options. IMPORTANT: You may need to close and restart your shell after running 'conda init'. Traceback (most recent call last): File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run self._run() File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run resultFiles = self._runFunc() File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc return self._func(*self._args) File "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", line 135, in preprocess self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), tomoFile, tomo.getSamplingRate()), File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1454, in runJob self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob process.runJob(log, programName, params, File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob return runCommand(command, env, cwd) File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ' conda activate emantomo-2.91_211111 && e2proc3d.py Runs/000002_ProtImportTomograms/extra/overview_wbp.em /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc --apix=5.000000' returned non-zero exit status 1. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Lugmayr, W. <w.l...@uk...> - 2022-07-13 14:09:04
|
Dear Hong, maybe it was not so clear, but the conda activation is in the PLUGINS section below the PYWORKFLOW in the config file. In our case: : [PLUGINS] CONDA_ACTIVATION_CMD = source /beegfs/cssb/software/em/scipion/3.0/miniconda/etc/profile.d/conda.sh EM_ROOT = software/em : CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 : Cheers, Wolfgang From: "Mailing list for Scipion users" <sci...@li...> To: "Mailing list for Scipion users" <sci...@li...> Cc: "HONG ZHAN" <hz...@wi...> Sent: Wednesday, 13 July, 2022 15:14:35 Subject: [EXT] Re: [scipion-users] emantomo plugin install Thanks Grigory and David, I tried also adding the this line in scipion.conf, however the issue persisted. I also have installed eman2.91 before, it might miss things up. I will check my envs and if not, i will rebuild my system clean. Pesyg seems having same issue… Thank you so much for the reply. Bien cordialement, Hong On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...> wrote: BQ_BEGIN Dear Hong, It seems Scipion is not able to find the location of conda in your system, which is required to execute the programs integrated in emantomo. The easiest way to solve this issue is to add a new variable to the Scipion config file. This file should be located in path/to/your/scipion/config/scipion.conf The variable you will need is the following one (after the [PYWORKFLOW] section inside the file should be fine): CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)". Best, David On 12/7/22 20:43, HONG ZHAN via scipion-users wrote: BQ_BEGIN Hi all, I am trying to install emantomo plugin, however, it showed error message below, does anyone have idea how to solve this error? Super thanks! Hong -------------------- CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run $ conda init <SHELL_NAME> Currently supported shells are: - bash - fish - tcsh - xonsh - zsh - powershell See 'conda init --help' for more information and options. IMPORTANT: You may need to close and restart your shell after running 'conda init'. Traceback (most recent call last): File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run self._run() File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run resultFiles = self._runFunc() File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc return self._func(*self._args) File "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", line 135, in preprocess self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), tomoFile, tomo.getSamplingRate()), File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1454, in runJob self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob process.runJob(log, programName, params, File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob return runCommand(command, env, cwd) File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ' conda activate emantomo-2.91_211111 && e2proc3d.py Runs/000002_ProtImportTomograms/extra/overview_wbp.em /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc --apix=5.000000' returned non-zero exit status 1. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: 稲葉弘哲 <hi...@me...> - 2022-07-13 14:07:43
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Dear Hong As David mentioned, adding "CONDA_ACTIVATION_CMD" to the config was necessary for EMAN and Pyseg installation when I installed them. In my case, "CONDA_ACTIVATION_CMD = . /usr/local/miniconda/etc/profile.d/conda.sh" worked. See also Topaz integration in https://github.com/scipion-em/scipion-em-topaz Best, Hironori Hironori Inaba Ph.d. Department of Histology and Cell Biology, Graduate School of Medicine, Mie University, Japan e-mail: hi...@me... 2022年7月13日(水) 22:16 HONG ZHAN via scipion-users < sci...@li...>: > Thanks Grigory and David, > > I tried also adding the this line in scipion.conf, however the issue > persisted. I also have installed eman2.91 before, it might miss things up. > I will check my envs and if not, i will rebuild my system clean. > > Pesyg seems having same issue… > > Thank you so much for the reply. > > Bien cordialement, > Hong > > On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...> wrote: > > > > Dear Hong, > > > It seems Scipion is not able to find the location of conda in your system, > which is required to execute the programs integrated in emantomo. > > > The easiest way to solve this issue is to add a new variable to the > Scipion config file. This file should be located in > path/to/your/scipion/config/scipion.conf > > > The variable you will need is the following one (after the [PYWORKFLOW] > section inside the file should be fine): CONDA_ACTIVATION_CMD = eval > "$(/path/to/your/conda/condabin/conda shell.bash hook)". > > > Best, > > > David > > > On 12/7/22 20:43, HONG ZHAN via scipion-users wrote: > > Hi all, > > I am trying to install emantomo plugin, however, it showed error message > below, does anyone have idea how to solve this error? > > Super thanks! > Hong > > -------------------- > CommandNotFoundError: Your shell has not been properly configured to use > 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > 'conda init'. > > > Traceback (most recent call last): > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 201, in run > self._run() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 252, in _run > resultFiles = self._runFunc() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _runFunc > return self._func(*self._args) > File > "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", > line 135, in preprocess > self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), > tomoFile, tomo.getSamplingRate()), > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1454, in runJob > self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > process.runJob(log, programName, params, > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > return runCommand(command, env, cwd) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line > 364, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command ' conda activate > emantomo-2.91_211111 && e2proc3d.py > Runs/000002_ProtImportTomograms/extra/overview_wbp.em > /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc > --apix=5.000000' returned non-zero exit status 1. > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: HONG Z. <hz...@wi...> - 2022-07-13 13:14:53
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Thanks Grigory and David,
I tried also adding the this line in scipion.conf, however the issue persisted. I also have installed eman2.91 before, it might miss things up. I will check my envs and if not, i will rebuild my system clean.
Pesyg seems having same issue…
Thank you so much for the reply.
Bien cordialement,
Hong
On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...> wrote:
Dear Hong,
It seems Scipion is not able to find the location of conda in your system, which is required to execute the programs integrated in emantomo.
The easiest way to solve this issue is to add a new variable to the Scipion config file. This file should be located in path/to/your/scipion/config/scipion.conf
The variable you will need is the following one (after the [PYWORKFLOW] section inside the file should be fine): CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)".
Best,
David
On 12/7/22 20:43, HONG ZHAN via scipion-users wrote:
Hi all,
I am trying to install emantomo plugin, however, it showed error message below, does anyone have idea how to solve this error?
Super thanks!
Hong
--------------------
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Traceback (most recent call last):
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
self._run()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
resultFiles = self._runFunc()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
return self._func(*self._args)
File "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", line 135, in preprocess
self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), tomoFile, tomo.getSamplingRate()),
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1454, in runJob
self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
process.runJob(log, programName, params,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
return runCommand(command, env, cwd)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' conda activate emantomo-2.91_211111 && e2proc3d.py Runs/000002_ProtImportTomograms/extra/overview_wbp.em /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc --apix=5.000000' returned non-zero exit status 1.
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: David H. <dhe...@cn...> - 2022-07-13 06:42:54
|
Dear Hong, It seems Scipion is not able to find the location of conda in your system, which is required to execute the programs integrated in emantomo. The easiest way to solve this issue is to add a new variable to the Scipion config file. This file should be located in path/to/your/scipion/config/scipion.conf The variable you will need is the following one (after the [PYWORKFLOW] section inside the file should be fine): CONDA_ACTIVATION_CMD = eval "$(/path/to/your/conda/condabin/conda shell.bash hook)". Best, David On 12/7/22 20:43, HONG ZHAN via scipion-users wrote: > Hi all, > > I am trying to install emantomo plugin, however, it showed error > message below, does anyone have idea how to solve this error? > > Super thanks! > Hong > > -------------------- > CommandNotFoundError: Your shell has not been properly configured to > use 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > 'conda init'. > > > Traceback (most recent call last): > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 201, in run > self._run() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 252, in _run > resultFiles = self._runFunc() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _runFunc > return self._func(*self._args) > File > "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", > line 135, in preprocess > self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), > tomoFile, tomo.getSamplingRate()), > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1454, in runJob > self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > process.runJob(log, programName, params, > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > return runCommand(command, env, cwd) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", > line 364, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command ' conda activate > emantomo-2.91_211111 && e2proc3d.py > Runs/000002_ProtImportTomograms/extra/overview_wbp.em > /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc > --apix=5.000000' returned non-zero exit status 1. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2022-07-12 21:59:32
|
There are 2 main elements involved: 1.- name of the conda environment 2.- name of the launcher (scipion3) For 1, you have the option to specify a name for the conda environment to be used with scipion. See https://pypi.org/project/scipion-installer/ (it will be using the -n argument) Then for the launcher there is no parameter but just renaming it should work. Be aware that every new installation, will require all the plugins again and a config file (that could be copied from the previous installation Be aware that since we have released scipion3 all updates are minor updates and with less risk than a full release. You can consider them patches. On 12/7/22 17:26, Biertuempfel, Christian (NIH/NHLBI) [E] via scipion-users wrote: > > Hi, > > Is it possible to pass a name to the conda install of scipion? I can > give a directory name but it will always end up with <dir>/scipion3. > > I would like to do something like <dir>/scipion3-220712 as we keep old > versions of software in case a user has trouble with running legacy > files/data. > > Cheers, > > christian > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Grigory S. <sha...@gm...> - 2022-07-12 18:46:34
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Hi, you have to open this test project and check the error in the stderr.log tab for the failed protocol. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Tue, Jul 12, 2022 at 7:43 PM HONG ZHAN via scipion-users < sci...@li...> wrote: > Hi all, > > I am trying to install emantomo plugin, however, it showed error message > below, does anyone have idea how to solve this error? > > Super thanks! > Hong > > -------------------- > CommandNotFoundError: Your shell has not been properly configured to use > 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > - bash > - fish > - tcsh > - xonsh > - zsh > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > 'conda init'. > > > Traceback (most recent call last): > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 201, in run > self._run() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 252, in _run > resultFiles = self._runFunc() > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _runFunc > return self._func(*self._args) > File > "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", > line 135, in preprocess > self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), > tomoFile, tomo.getSamplingRate()), > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 1454, in runJob > self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", > line 65, in runJob > process.runJob(log, programName, params, > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > return runCommand(command, env, cwd) > File > "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, > File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line > 364, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command ' conda activate > emantomo-2.91_211111 && e2proc3d.py > Runs/000002_ProtImportTomograms/extra/overview_wbp.em > /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc > --apix=5.000000' returned non-zero exit status 1. > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: HONG Z. <hz...@wi...> - 2022-07-12 18:43:27
|
Hi all,
I am trying to install emantomo plugin, however, it showed error message below, does anyone have idea how to solve this error?
Super thanks!
Hong
--------------------
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Traceback (most recent call last):
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
self._run()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
resultFiles = self._runFunc()
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
return self._func(*self._args)
File "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", line 135, in preprocess
self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), tomoFile, tomo.getSamplingRate()),
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1454, in runJob
self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
process.runJob(log, programName, params,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
return runCommand(command, env, cwd)
File "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' conda activate emantomo-2.91_211111 && e2proc3d.py Runs/000002_ProtImportTomograms/extra/overview_wbp.em /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc --apix=5.000000' returned non-zero exit status 1.
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From: Grigory S. <sha...@gm...> - 2022-07-12 17:24:03
|
Hi Christian, Yes, there's an option -n name for the installer. You can check with -h for the list of options On Tue, Jul 12, 2022, 16:42 Biertuempfel, Christian (NIH/NHLBI) [E] via scipion-users <sci...@li...> wrote: > > > Hi, > > Is it possible to pass a name to the conda install of scipion? I can give > a directory name but it will always end up with <dir>/scipion3. > > I would like to do something like <dir>/scipion3-220712 as we keep old > versions of software in case a user has trouble with running legacy > files/data. > > > > Cheers, > > christian > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: HONG Z. <hz...@wi...> - 2022-07-12 15:46:35
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Hi Grigory, SUper thanks! It works! Bien cordialement, Hong ________________________________ From: Grigory Sharov <sha...@gm...> Sent: Tuesday, July 12, 2022 10:37 AM To: Mailing list for Scipion users <sci...@li...> Cc: HONG ZHAN <hz...@wi...> Subject: Re: [scipion-users] Question about scipion3 relion test failure Dear Hong, There's no test with such a name. You can get the list of tests by running: scipion3 test --grep relion Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Tue, Jul 12, 2022 at 4:30 PM HONG ZHAN via scipion-users <sci...@li...<mailto:sci...@li...>> wrote: Dear Scipion group, My name is Hong Zhan and research scientist at the University of Wisconsin-Madison. I am recently trying out Scipion-tomo package on my CryoET project. I am very interested in the workflow and particularly am interested in pyseg. Os: Ubuntu 20.0.4; scipion-em updated version. I installed the scipion3 and along with plugins. However, it seems my relion related tests failed. But Cistem and others are fine. Would be great to have some help on the issues. I have relion3 and relion4 enabled. But it seems not find the relion test file, would be name changed? Super thanks! Hong _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Biertuempfel, C. (NIH/N. [E]
<chr...@ni...> - 2022-07-12 15:42:29
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Hi, Is it possible to pass a name to the conda install of scipion? I can give a directory name but it will always end up with <dir>/scipion3. I would like to do something like <dir>/scipion3-220712 as we keep old versions of software in case a user has trouble with running legacy files/data. Cheers, christian |
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