scipion-users — Mailing list for Scipion users

Re: [scipion-users] K3 tiff format movies

[Gregory S. <sha...@gm...>]

Hi,

K3 gain/dark reference stability is still a problem I believe (especially
in CDS mode), so I am not surprised that you do it every gridsquare.
Acquiring a new gain takes 15-20 min on K3.

The workaround in scipion would be to import every gridsqaure separately
and run motioncor2, then join the outputs.

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, Sep 24, 2019 at 11:00 PM Carlos Oscar S. Sorzano <co...@cn...>
wrote:

> Dear Nora,
>
>
> the current Scipion model does not allow for several gain images. Have you
> found a situation where this is needed or customary? We understand that
> collecting the gain image takes about 1h, if not more, is that correct?
>
>
> Kind regards, Carlos Oscar
>
>
> El 23/09/2019 a las 16:49, Nora Cronin escribió:
>
> Hi
>
> I am attempting to process K3 "tiff LZW non gain normalised" movies in
> Scipion.     There is one gain reference file included in each gridsquare
> directory.       In the import GUI I input the name of the directory
> /Gridsquare*/Data   and for the Pattern "*_fractions.tiff ".
> Since the name of the gain is different in each Gridsquare - how do I
> input the gain There is one gain reference for all the movies in that
> particular grid square    Inputing the one gain reference in the
> Gridsquare/Data subdirectory did not work - motioncorr did not find the
> gain reference after the first movie.
>
> Should I use the gain reference directly form DM (the .dm4) file and if so
> how should I convert it?
>
> Best regards
>
>
> Nora
>
> Nora Cronin
> LonCEM Facility Manager
>
> The Francis Crick Institute
>
> 1 Midland Road
>
> London NW1 1AT
>
>
> T: +4420379*65225*
>
> E: nor...@cr... <ali...@cr...>
>
> W: www.crick.ac.uk
>
> The Francis Crick Institute Limited is a registered charity in England and
> Wales no. 1140062 and a company registered in England and Wales no.
> 06885462, with its registered office at 1 Midland Road London NW1 1AT
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> ------------------------------------------------------------------------
> Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
> Biocomputing unit                             http://i2pc.es/coss
> National Center of Biotechnology (CSIC)
> c/Darwin, 3
> Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
> 28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
> ------------------------------------------------------------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] K3 tiff format movies

[Carlos O. S. S. <co...@cn...>]

Dear Nora,


the current Scipion model does not allow for several gain images. Have 
you found a situation where this is needed or customary? We understand 
that collecting the gain image takes about 1h, if not more, is that correct?


Kind regards, Carlos Oscar


El 23/09/2019 a las 16:49, Nora Cronin escribió:
> Hi
>
> I am attempting to process K3 "tiff LZW non gain normalised" movies in 
> Scipion.     There is one gain reference file included in each 
> gridsquare directory.       In the import GUI I input the name of the 
> directory /Gridsquare*/Data   and for the Pattern "*_fractions.tiff ".
> Since the name of the gain is different in each Gridsquare - how do I 
> input the gain There is one gain reference for all the movies in that 
> particular grid square    Inputing the one gain reference in the 
> Gridsquare/Data subdirectory did not work - motioncorr did not find 
> the gain reference after the first movie.
>
> Should I use the gain reference directly form DM (the .dm4) file and 
> if so how should I convert it?
>
> Best regards
>
>
> Nora
> Nora Cronin
> LonCEM Facility Manager
>
> The Francis Crick Institute
>
> 1 Midland Road
>
> London NW1 1AT
>
>
> T: +4420379*65225*
>
> E: nor...@cr... <mailto:ali...@cr...>
>
> W: www.crick.ac.uk <http://www.crick.ac.uk/>
>
> The Francis Crick Institute Limited is a registered charity in England 
> and Wales no. 1140062 and a company registered in England and Wales 
> no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
------------------------------------------------------------------------

Re: [scipion-users] using MonoRes from command line

[JOSE L. V. P. <jl...@cn...>]

Dear Gabriella,

Thank you for your interest in MonoRes.

Most of algorithm that are integrated in Scipion can run with a  
command line, in particular MonoRes.

To run MonoRes, first you need Xmipp installed in your  
computer/machine (probably it is already installed if you use Scipion,  
if not...

Here you can fin the instructions: https://github.com/I2PC/xmipp

Once you hace installed Xmipp its time to run MonoRes. To do that  
first Xmipp enviroment need to be loaded

1. Load Xmipp enviroment, executing next command (you have to  
substitute the path)

source /folderWhereXmippIsInstalled/build/xmipp.bashrc

2. Run MonoRes comand with your data, for example (Detailed  
instructions will be given below)

xmipp_resolution_monogenic_signal  --vol betaGal.mrc:mrc --mask  
binarized_mask.mrc --sampling_rate 3.540000 --minRes 1.000000 --maxRes  
25.000000 --step 0.250000 --mask_out  
Runs/000214_XmippProtMonoRes/extra/output_Mask.mrc -o mgresolution.mrc  
--volumeRadius 50.000000 --exact --chimera_volume  
MG_Chimera_resolution.mrc --sym c1 --significance 0.950000  
--md_outputdata mask_data.xmd

-----------------------------------------------------
%% Specific information about MonoRes
IMPORTANT: MonoRes requires that your maps present noise otherwise it  
is not able to compute the local resolution of the map. The  
alternative is the map is nosie free, is the use of two half maps.

MonoRes requires next fields to run (for a single map):

xmipp_resolution_monogenic_signal

--vol            File name of the map to estimate its resolution
--mask           File name of a binary mask that define where the  
protein is. Outside the mask there is only noise. It defines the  
boundary between noise and protein.
--sampling_rate  Pixel size of your protein
--minRes         The highest resolution (you can set to 0.5A)
--maxRes         The lowest resolution. probably you will work at high  
resolution, so you can set it to 8A
--step           [By default 0.25A] Local resolution will be analyzed  
in steps of the given number, for instance
--mask_out       This is not important for you. The provided mask is  
refined by MonoRes. It is an output of MonoRes. Just right a file name  
like outputmask.mrc
-o
--volumeRadius   This is important, many maps present areas free of  
noise (usually they are out of a sphere), this radiues tells MonoRes  
the radius of that sphere. If the map is not masked with an sphere,  
then this volume radius is the half of the boxsize.
--exact          It is a flag about the algorithm just write it
--chimera_volume MonoRes produces a map for the visualization in  
chimera. So provide the file name for that, for instance  
chimeraResolution.mrc.
--sym            In the first verion of MonoRes symmetry was required,  
now you can set it as c1
--significance   The significance for statistical calculus, set it to 0.95
--md_outputdata  This is a metadata created for scipion nor relevant  
for you. Just write a file name metadata.xmd
ammaple:
xmipp_resolution_monogenic_signal  --vol betaGal.mrc:mrc --mask  
binarized_mask.mrc --sampling_rate 3.540000 --minRes 1.000000 --maxRes  
25.000000 --step 0.250000 --mask_out  
Runs/000214_XmippProtMonoRes/extra/output_Mask.mrc -o mgresolution.mrc  
--volumeRadius 50.000000 --exact --chimera_volume  
MG_Chimera_resolution.mrc --sym c1 --significance 0.950000  
--md_outputdata mask_data.xmd

More considerations:

As you can see, MonoRes requires a binary mask for running. The  
creation of such mask must be carried out before running MonoRes as it  
follows

First, known the boxsize of the map, the map is filtered with a  
gaussian kernel

setSize = 0.02*boxsize

xmipp_transform_filter -i volumeFileName --fourier real_gaussian  
setSize -o gaussianMapFileName

Then, the filtered map is thresholded to obtain a binary mask. It  
requires to determine the maximum intensity of the map

max_val = 0.05*max(gaussianMapFileName)

xmipp_transform_threshold -i gaussianMapFileName --select below  
max_val --substitute binarize -o binaryMaskFileName

Please feel you free and do not hesitate of asking anything you want.  
I know that in a first approach it can seem complex, but it is not,  
trust me.

Kind regards

Jose Luis Vilas



Quoting Pablo Conesa <pc...@cn...>:

> Sorry Gabriella for the late reply....your email was stuck in the admin site.
>
> Scipion is written in python and you can almost do anything from a  
> python script. Let me know if you'd like to try this idea.
>
> Now, monores is part of xmipp and there is a program (binary behind)  
> but not sure if calling it from a terminal will render what you get.
>
> Best person to answer is Jose Luis, I think he is reading this list.  
> He might be able to help you.
>
> On 28/8/19 19:41, Gabriella Reggiano wrote:
>> Hi all,
>>
>> I have been looking for alternatives to ResMap because I need to  
>> calculate resolution estimates for a large number of maps, and I  
>> wanted something that required very little user input (ideally,  
>> without masks). MonoRes is the closest to what I need. Do you have  
>> any advice for getting MonoRes/Scipion to run through the command  
>> line, rather than the GUI?
>>
>> Thank you,
>> Gabriella Reggiano
>> --
>> Ph.D. Student
>> DiMaio Lab
>> Department of Biochemistry
>> University of Washington
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] using MonoRes from command line

[Pablo C. <pc...@cn...>]

Sorry Gabriella for the late reply....your email was stuck in the admin 
site.

Scipion is written in python and you can almost do anything from a 
python script. Let me know if you'd like to try this idea.

Now, monores is part of xmipp and there is a program (binary behind) but 
not sure if calling it from a terminal will render what you get.

Best person to answer is Jose Luis, I think he is reading this list. He 
might be able to help you.

On 28/8/19 19:41, Gabriella Reggiano wrote:
> Hi all,
>
> I have been looking for alternatives to ResMap because I need to 
> calculate resolution estimates for a large number of maps, and I 
> wanted something that required very little user input (ideally, 
> without masks). MonoRes is the closest to what I need. Do you have any 
> advice for getting MonoRes/Scipion to run through the command line, 
> rather than the GUI?
>
> Thank you,
> Gabriella Reggiano
> --
> Ph.D. Student
> DiMaio Lab
> Department of Biochemistry
> University of Washington
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] K3 tiff format movies

[Pablo C. <pc...@cn...>]

Hi Nora!


All users I know they are using the dm4 gain and one gain per import. I 
personally do not see the benefit of having a gain per movie/gridsquare. 
Although I might be wrong and it might

be something actually useful to have.


Scipion will do the convertion from dm4 to mrc, so you don't need to 
bother with format conversions.


There is one thing you might want to check, and is the gain orientation, 
so far you need to flip it on Y if your gain is dm4.


For a quick check, make a subset of the movies with one movie an apply 
ply with that movie, motioncor and the the orientation.


If the gain is very subtle, I haven't found a way to verify the 
orientation, in that case I would set "Flip gain reference" to "upside down"



Bear in mind that you need to activate the "Advanced mode" to display 
that field.


All the best, Pablo.


On 23/9/19 16:49, Nora Cronin wrote:
> Hi
>
> I am attempting to process K3 "tiff LZW non gain normalised" movies in 
> Scipion.     There is one gain reference file included in each 
> gridsquare directory.       In the import GUI I input the name of the 
> directory /Gridsquare*/Data   and for the Pattern "*_fractions.tiff ".
> Since the name of the gain is different in each Gridsquare - how do I 
> input the gain There is one gain reference for all the movies in that 
> particular grid square    Inputing the one gain reference in the 
> Gridsquare/Data subdirectory did not work - motioncorr did not find 
> the gain reference after the first movie.
>
> Should I use the gain reference directly form DM (the .dm4) file and 
> if so how should I convert it?
>
> Best regards
>
>
> Nora
> Nora Cronin
> LonCEM Facility Manager
>
> The Francis Crick Institute
>
> 1 Midland Road
>
> London NW1 1AT
>
>
> T: +4420379*65225*
>
> E: nor...@cr... <mailto:ali...@cr...>
>
> W: www.crick.ac.uk <http://www.crick.ac.uk/>
>
> The Francis Crick Institute Limited is a registered charity in England 
> and Wales no. 1140062 and a company registered in England and Wales 
> no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
>
>
>
> _______________________________________________
> 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] K3 tiff format movies

[Nora C. <nor...@cr...>]

Hi

I am attempting to process K3 "tiff LZW non gain normalised" movies in Scipion.     There is one gain reference file included in each gridsquare directory.       In the import GUI I input the name of the directory /Gridsquare*/Data   and for the Pattern "*_fractions.tiff ".
Since the name of the gain is different in each Gridsquare - how do I input the gain There is one gain reference for all the movies in that particular grid square    Inputing the one gain reference in the Gridsquare/Data subdirectory did not work - motioncorr did not find the gain reference after the first movie.

Should I use the gain reference directly form DM (the .dm4) file and if so how should I convert it?

Best regards


Nora

Nora Cronin
LonCEM Facility Manager

The Francis Crick Institute

1 Midland Road

London NW1 1AT


T: +442037965225

E: nor...@cr...<mailto:ali...@cr...>

W: www.crick.ac.uk<http://www.crick.ac.uk/>

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[scipion-users] using MonoRes from command line

[Gabriella R. <reg...@uw...>]

Hi all,

I have been looking for alternatives to ResMap because I need to calculate
resolution estimates for a large number of maps, and I wanted something
that required very little user input (ideally, without masks). MonoRes is
the closest to what I need. Do you have any advice for getting
MonoRes/Scipion to run through the command line, rather than the GUI?

Thank you,
Gabriella Reggiano
--
Ph.D. Student
DiMaio Lab
Department of Biochemistry
University of Washington

Re: [scipion-users] DM4 to MRC conversion flips gain reference?

[Pablo C. <pc...@cn...>]

<div dir='auto'>hi Matt, since motioncor does not accept dm4, scipion is using xmipp to convert dm4 to mrc and there, the flip on Y is happening.&nbsp;<div dir="auto"><br></div><div dir="auto">We will try to investigate more, but meanwhile:</div><div dir="auto"><br></div><div dir="auto">Gain in dm4 will require flip on Y in motioncor 2, and I guess the rest of the alignment protocols.</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 28 ago. 2019 1:16, Matt Harrington &lt;ma...@ms...&gt; escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Our users report that the motioncor2 protocol flips the gain reference&#13;<br>
when converting from .dm4 to .mrc.&nbsp; I see an option in the MC2&#13;<br>
protocol to flip the gain reference back.&nbsp; However, I'm wondering why&#13;<br>
the gain reference is flipped in the first place.&#13;<br>
&#13;<br>
This code seems relevant:&#13;<br>
&#13;<br>
https://github.com/I2PC/scipion/blob/d1a60f69960d1079bbbecde5bf3f5f4017b36927/pyworkflow/em/convert/image_handler.py#L178&#13;<br>
&#13;<br>
However, since *.img files are not involved I would guess the "else"&#13;<br>
branch of that statement would be followed, meaning that Xmipp&#13;<br>
performs the conversion.&#13;<br>
&#13;<br>
Any ideas how to troubleshoot this?&#13;<br>
&#13;<br>
Matt&#13;<br>
&#13;<br>
&#13;<br>
_______________________________________________&#13;<br>
scipion-users mailing list&#13;<br>
sci...@li...&#13;<br>
https://lists.sourceforge.net/lists/listinfo/scipion-users&#13;<br>
</p>
</blockquote></div><br></div>

[scipion-users] DM4 to MRC conversion flips gain reference?

[Matt H. <ma...@ms...>]

Our users report that the motioncor2 protocol flips the gain reference
when converting from .dm4 to .mrc.  I see an option in the MC2
protocol to flip the gain reference back.  However, I'm wondering why
the gain reference is flipped in the first place.

This code seems relevant:

https://github.com/I2PC/scipion/blob/d1a60f69960d1079bbbecde5bf3f5f4017b36927/pyworkflow/em/convert/image_handler.py#L178

However, since *.img files are not involved I would guess the "else"
branch of that statement would be followed, meaning that Xmipp
performs the conversion.

Any ideas how to troubleshoot this?

Matt

Re: [scipion-users] Bug --> xmipp-picking consensus protocol

[Pablo C. <pc...@cn...>]

Double thanks Dmitry for reporting the big and providing a workaround.

One of the xmipp developers is been working on this and might be even be 
fixed in the next xmipp release.


On 22/8/19 11:07, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> The bug.
>
> ####
>
> *_Description_*
>
> *__*
>
> The bug causes stop of the *xmipp-picking consensus* protocol if one 
> of the comparison sets has 0 particle in any of its micrograph.
>
> ####
>
> *_Location_*
>
> *xmipp-picking consensus*protocol
>
> ####
>
> *_Temporal solution_*
>
> *__*
>
>  1. Look through all the particles in the *scipion-extract coordinates
>     *protocol. (The output of this protocol goes to *xmipp-picking
>     consensus* protocol).
>  2. Find  ‘Available’ column ( the last one).
>  3. Add 1 particle in every ‘Available’ micrograph. The micrograph
>     will change the name to ‘Manual’
>  4. Save the coordinates pressing ‘Coordinates’ button
>  5. Use the *xmipp-picking consensus* as usual àNow everything should work
>
> Sincerely,
>
> Dmitry
>
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] Bug --> xmipp-picking consensus protocol

[Dmitry S. <sem...@gm...>]

Dear colleagues, 

 

The bug.

 

####

Description

 

The bug causes stop of the xmipp-picking consensus protocol if one of the comparison sets has 0 particle in any of its micrograph.

 

####

Location

xmipp-picking consensus protocol

 

####

Temporal solution

 
Look through all the particles in the scipion-extract coordinates protocol. (The output of this protocol goes to xmipp-picking consensus protocol).
Find  ‘Available’ column ( the last one).
Add 1 particle in every ‘Available’ micrograph. The micrograph will change the name to ‘Manual’
Save the coordinates pressing ‘Coordinates’ button
Use the xmipp-picking consensus as usual à Now everything should work
 

 

Sincerely,

Dmitry

Re: [scipion-users] Installation problems (WSL)

[Pablo C. <pc...@cn...>]

This is starting to ring a bell....I've searched my emails but couldn't 
find anything, but may be is related to some ssh library missing?

I might not be able to explain it but I think python installation 
requires some ssl libraries (optionally) that latter on will be critical 
for installing other packages.


Could you please have a look at the python installation log files at:

<scipion_home>/software/log/python_*

May be there is something there that could give us a hint?


On 14/8/19 10:37, Viktor Bengtsson wrote:
>
> When I import Queue I get the result
>
> <module 'Queue' from 
> '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Queue/__init__.pyc'>
>
> I also tried the “from pip._internal” line from the traceback posted 
> previously, and got the same error as before.
>
> So either the problem is having Queue as a module installed along with 
> the rest, or there is something else. There seems to be something 
> strange going on with urllib3.
>
> Thank you for all the patience,
>
> Viktor
>
> *From:*Pablo Conesa <pc...@cn...>
> *Sent:* den 14 augusti 2019 08:54
> *To:* sci...@li...
> *Subject:* Re: [scipion-users] Installation problems (WSL)
>
> I guess changes of this 
> (https://github.com/python-zk/kazoo/issues/239) being your case are 
> low, but just in case?
>
> On 13/8/19 15:51, Viktor Bengtsson wrote:
>
>     Thanks for the suggestion. Unfortunately I get the same error:
>
>     /mnt/e/Linux_programs/scipion$ scipion python -m pip install requests
>
>     Scipion v2.0 (2019-04-23) Diocletian
>
>     >>>>> python  "-m" "pip" "install" "requests"
>
>     Traceback (most recent call last):
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>     line 174, in _run_module_as_main
>
>     "__main__", fname, loader, pkg_name)
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>     line 72, in _run_code
>
>     exec code in run_globals
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py",
>     line 16, in <module>
>
>     from pip._internal import main as _main  # isort:skip # noqa
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py",
>     line 19, in <module>
>
>     from pip._vendor.urllib3.exceptions import DependencyWarning
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py",
>     line 8, in <module>
>
>     from .connectionpool import (
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py",
>     line 44, in <module>
>
>     from .util.queue import LifoQueue
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py",
>     line 7, in <module>
>
>     import Queue as _unused_module_Queue  # noqa: F401
>
>     File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py",
>     line 10, in <module>
>
>     class LifoQueue(queue.Queue):
>
>     AttributeError: 'module' object has no attribute 'Queue'
>
>     Kind regards,
>
>     Viktor
>
>     *From:*Pablo Conesa <pc...@cn...>
>     <mailto:pc...@cn...>
>     *Sent:* den 13 augusti 2019 14:40
>     *To:* sci...@li...
>     <mailto:sci...@li...>
>     *Subject:* Re: [scipion-users] Installation problems (WSL)
>
>     What if you do:
>
>     scipion python -m pip install requests
>
>     On 13/8/19 13:18, Viktor Bengtsson wrote:
>
>         Hi,
>
>         I tried what you suggested, but nothing seems to work. All
>         packages installed prior to requests seem to install properly,
>         so I wonder if there is something in particular related to
>         that package that causes an error. Alternatively, is there
>         some workaround to install that package into site-packages
>         without using pip included with the installation of Scipion?
>
>         Kind regards,
>
>         Viktor
>
>         *From:*Lugmayr, Wolfgang <w.l...@uk...>
>         <mailto:w.l...@uk...>
>         *Sent:* den 12 augusti 2019 16:47
>         *To:* Mailing list for Scipion users
>         <sci...@li...>
>         <mailto:sci...@li...>
>         *Subject:* Re: [scipion-users] Installation problems (WSL)
>
>         hi,
>
>         maybe your os python is mixed up with the scipion one:
>
>         can you check the following environment variables and test to
>         set the scipion path first?
>
>         LD_LIBRARY_PATH /whereever.../scipion/software/lib
>         PYTHONPATH /whereever.../scipion/software/lib
>
>         cheers,
>
>         wolfgang
>
>         ------------------------------------------------------------------------
>
>         *From: *"Viktor Bengtsson" <vik...@mm...
>         <mailto:vik...@mm...>>
>         *To: *"Mailing list for Scipion users"
>         <sci...@li...
>         <mailto:sci...@li...>>
>         *Sent: *Monday, 12 August, 2019 14:49:20
>         *Subject: *[scipion-users] Installation problems (WSL)
>
>         Dear all,
>
>         Before summer I could use Scipion without problem. However,
>         after vacation (and possibly some change in environment) it
>         would not start at all. Unfortunately I did not save the error
>         message before trying to reinstall, and reinstallation does
>         not seem to work at all.
>
>         The initial attempt was made on Ubuntu 16.04 installed through
>         WSL on my work computer. I also tried installing on Ubuntu
>         18.04 installed on WSL on my home computer (where I have not
>         used WSL at all previously, so no prior python installation).
>         In all cases there have been a number of problems compiling
>         python packages, and I can’t start Scipion.
>
>         I followed the instructions found at
>         https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install,
>         both for “From Binaries” and “Sources from GitHub”. The
>         attached log files should include all input and all output.
>
>         Does anyone know what might be the problem?
>
>         Kind regards,
>
>         Viktor Bengtsson
>
>         PhD student
>
>         Stockholm University
>
>         PS. The final error I get when attempting to install from
>         sources is :
>
>         /mnt/e/Linux_programs/scipion/scipion/software/bin/python
>         /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>         install requests==2.18.4
>
>         Traceback (most recent call last):
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>         line 174, in _run_module_as_main
>
>             "__main__", fname, loader, pkg_name)
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>         line 72, in _run_code
>
>             exec code in run_globals
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py",
>         line 16, in <module>
>
>             from pip._internal import main as _main  # isort:skip # noqa
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py",
>         line 19, in <module>
>
>             from pip._vendor.urllib3.exceptions import DependencyWarning
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py",
>         line 7, in <module>
>
>             from .connectionpool import (
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py",
>         line 45, in <module>
>
>             from .util.queue import LifoQueue
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py",
>         line 7, in <module>
>
>             import Queue as _unused_module_Queue  # noqa: F401
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py",
>         line 10, in <module>
>
>             class LifoQueue(queue.Queue):
>
>         AttributeError: 'module' object has no attribute 'Queue'
>
>         Error: target
>         '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests'
>         not built (after running
>         '/mnt/e/Linux_programs/scipion/scipion/software/bin/python
>         /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>         install requests==2.18.4')
>
>         The original error (that reoccurred after installing from
>         binaries) is:
>
>         user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion
>
>         Scipion v2.0 (2019-04-23) Diocletian
>
>         >>>>> python /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
>
>         Traceback (most recent call last):
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py",
>         line 32, in <module>
>
>             from pyworkflow.gui.project import ProjectManagerWindow
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py",
>         line 27, in <module>
>
>             from gui import *
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py",
>         line 29, in <module>
>
>             import Tkinter as tk
>
>           File
>         "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py",
>         line 6, in <module>
>
>             from Tkinter import (_cnfmerge, _default_root, _flatten,
>
>         ImportError: cannot import name _cnfmerge
>
>
>
>         _______________________________________________
>         scipion-users mailing list
>         sci...@li...
>         <mailto:sci...@li...>
>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>         sers">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
>
>     > 
>
>     ot;Times New Roman",serif;color:windowtext;mso-fareast-language:SV">>
>
>
>     _______________________________________________
>
>     scipion-users mailing list
>
>     sci...@li...  <mailto:sci...@li...>
>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
> ablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
> strong>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*

Re: [scipion-users] Installation problems (WSL)

[Viktor B. <vik...@mm...>]

When I import Queue I get the result
<module 'Queue' from '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Queue/__init__.pyc'>

I also tried the “from pip._internal” line from the traceback posted previously, and got the same error as before.

So either the problem is having Queue as a module installed along with the rest, or there is something else. There seems to be something strange going on with urllib3.

Thank you for all the patience,
Viktor


From: Pablo Conesa <pc...@cn...>
Sent: den 14 augusti 2019 08:54
To: sci...@li...
Subject: Re: [scipion-users] Installation problems (WSL)


I guess changes of this (https://github.com/python-zk/kazoo/issues/239) being your case are low, but just in case?


On 13/8/19 15:51, Viktor Bengtsson wrote:
Thanks for the suggestion. Unfortunately I get the same error:

/mnt/e/Linux_programs/scipion$ scipion python -m pip install requests

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  "-m" "pip" "install" "requests"
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 8, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 44, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'

Kind regards,
Viktor

From: Pablo Conesa <pc...@cn...><mailto:pc...@cn...>
Sent: den 13 augusti 2019 14:40
To: sci...@li...<mailto:sci...@li...>
Subject: Re: [scipion-users] Installation problems (WSL)


What if you do:

scipion python -m pip install requests
On 13/8/19 13:18, Viktor Bengtsson wrote:
Hi,
I tried what you suggested, but nothing seems to work. All packages installed prior to requests seem to install properly, so I wonder if there is something in particular related to that package that causes an error. Alternatively, is there some workaround to install that package into site-packages without using pip included with the installation of Scipion?

Kind regards,
Viktor

From: Lugmayr, Wolfgang <w.l...@uk...><mailto:w.l...@uk...>
Sent: den 12 augusti 2019 16:47
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Subject: Re: [scipion-users] Installation problems (WSL)

hi,

maybe your os python is mixed up with the scipion one:

can you check the following environment variables and test to set the scipion path first?
LD_LIBRARY_PATH /whereever.../scipion/software/lib
PYTHONPATH /whereever.../scipion/software/lib
cheers,
wolfgang


________________________________
From: "Viktor Bengtsson" <vik...@mm...<mailto:vik...@mm...>>
To: "Mailing list for Scipion users" <sci...@li...<mailto:sci...@li...>>
Sent: Monday, 12 August, 2019 14:49:20
Subject: [scipion-users] Installation problems (WSL)

Dear all,
Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all.

The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can’t start Scipion.

I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install<https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install>, both for “From Binaries” and “Sources from GitHub”. The attached log files should include all input and all output.

Does anyone know what might be the problem?

Kind regards,
Viktor Bengtsson
PhD student
Stockholm University

PS. The final error I get when attempting to install from sources is :

/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'
Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4')

The original error (that reoccurred after installing from binaries) is:
user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module>
    import Tkinter as tk
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module>
    from Tkinter import (_cnfmerge, _default_root, _flatten,
ImportError: cannot import name _cnfmerge


_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
sers">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
>
ot;Times New Roman",serif;color:windowtext;mso-fareast-language:SV">>



_______________________________________________

scipion-users mailing list

sci...@li...<mailto:sci...@li...>

https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
ablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team

--
Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team
ablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team

Re: [scipion-users] Installation problems (WSL)

[Pablo C. <pc...@cn...>]

Sorry, chances not changes.

On 14/8/19 8:53, Pablo Conesa wrote:
>
> I guess changes of this 
> (https://github.com/python-zk/kazoo/issues/239) being your case are 
> low, but just in case?
>
>
> On 13/8/19 15:51, Viktor Bengtsson wrote:
>>
>> Thanks for the suggestion. Unfortunately I get the same error:
>>
>> /mnt/e/Linux_programs/scipion$ scipion python -m pip install requests
>>
>> Scipion v2.0 (2019-04-23) Diocletian
>>
>> >>>>> python  "-m" "pip" "install" "requests"
>>
>> Traceback (most recent call last):
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
>> line 174, in _run_module_as_main
>>
>> "__main__", fname, loader, pkg_name)
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
>> line 72, in _run_code
>>
>> exec code in run_globals
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", 
>> line 16, in <module>
>>
>> from pip._internal import main as _main  # isort:skip # noqa
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", 
>> line 19, in <module>
>>
>> from pip._vendor.urllib3.exceptions import DependencyWarning
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", 
>> line 8, in <module>
>>
>> from .connectionpool import (
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", 
>> line 44, in <module>
>>
>> from .util.queue import LifoQueue
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", 
>> line 7, in <module>
>>
>> import Queue as _unused_module_Queue  # noqa: F401
>>
>> File 
>> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", 
>> line 10, in <module>
>>
>> class LifoQueue(queue.Queue):
>>
>> AttributeError: 'module' object has no attribute 'Queue'
>>
>> Kind regards,
>>
>> Viktor
>>
>> *From:*Pablo Conesa <pc...@cn...>
>> *Sent:* den 13 augusti 2019 14:40
>> *To:* sci...@li...
>> *Subject:* Re: [scipion-users] Installation problems (WSL)
>>
>> What if you do:
>>
>> scipion python -m pip install requests
>>
>> On 13/8/19 13:18, Viktor Bengtsson wrote:
>>
>>     Hi,
>>
>>     I tried what you suggested, but nothing seems to work. All
>>     packages installed prior to requests seem to install properly, so
>>     I wonder if there is something in particular related to that
>>     package that causes an error. Alternatively, is there some
>>     workaround to install that package into site-packages without
>>     using pip included with the installation of Scipion?
>>
>>     Kind regards,
>>
>>     Viktor
>>
>>     *From:*Lugmayr, Wolfgang <w.l...@uk...>
>>     <mailto:w.l...@uk...>
>>     *Sent:* den 12 augusti 2019 16:47
>>     *To:* Mailing list for Scipion users
>>     <sci...@li...>
>>     <mailto:sci...@li...>
>>     *Subject:* Re: [scipion-users] Installation problems (WSL)
>>
>>     hi,
>>
>>     maybe your os python is mixed up with the scipion one:
>>
>>     can you check the following environment variables and test to set
>>     the scipion path first?
>>
>>     LD_LIBRARY_PATH /whereever.../scipion/software/lib
>>     PYTHONPATH /whereever.../scipion/software/lib
>>
>>     cheers,
>>
>>     wolfgang
>>
>>     ------------------------------------------------------------------------
>>
>>     *From: *"Viktor Bengtsson" <vik...@mm...
>>     <mailto:vik...@mm...>>
>>     *To: *"Mailing list for Scipion users"
>>     <sci...@li...
>>     <mailto:sci...@li...>>
>>     *Sent: *Monday, 12 August, 2019 14:49:20
>>     *Subject: *[scipion-users] Installation problems (WSL)
>>
>>     Dear all,
>>
>>     Before summer I could use Scipion without problem. However, after
>>     vacation (and possibly some change in environment) it would not
>>     start at all. Unfortunately I did not save the error message
>>     before trying to reinstall, and reinstallation does not seem to
>>     work at all.
>>
>>     The initial attempt was made on Ubuntu 16.04 installed through
>>     WSL on my work computer. I also tried installing on Ubuntu 18.04
>>     installed on WSL on my home computer (where I have not used WSL
>>     at all previously, so no prior python installation). In all cases
>>     there have been a number of problems compiling python packages,
>>     and I can’t start Scipion.
>>
>>     I followed the instructions found at
>>     https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install,
>>     both for “From Binaries” and “Sources from GitHub”. The attached
>>     log files should include all input and all output.
>>
>>     Does anyone know what might be the problem?
>>
>>     Kind regards,
>>
>>     Viktor Bengtsson
>>
>>     PhD student
>>
>>     Stockholm University
>>
>>     PS. The final error I get when attempting to install from sources
>>     is :
>>
>>     /mnt/e/Linux_programs/scipion/scipion/software/bin/python
>>     /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>>     install requests==2.18.4
>>
>>     Traceback (most recent call last):
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>>     line 174, in _run_module_as_main
>>
>>         "__main__", fname, loader, pkg_name)
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>>     line 72, in _run_code
>>
>>         exec code in run_globals
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py",
>>     line 16, in <module>
>>
>>         from pip._internal import main as _main  # isort:skip # noqa
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py",
>>     line 19, in <module>
>>
>>         from pip._vendor.urllib3.exceptions import DependencyWarning
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py",
>>     line 7, in <module>
>>
>>         from .connectionpool import (
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py",
>>     line 45, in <module>
>>
>>         from .util.queue import LifoQueue
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py",
>>     line 7, in <module>
>>
>>         import Queue as _unused_module_Queue  # noqa: F401
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py",
>>     line 10, in <module>
>>
>>         class LifoQueue(queue.Queue):
>>
>>     AttributeError: 'module' object has no attribute 'Queue'
>>
>>     Error: target
>>     '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests'
>>     not built (after running
>>     '/mnt/e/Linux_programs/scipion/scipion/software/bin/python
>>     /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>>     install requests==2.18.4')
>>
>>     The original error (that reoccurred after installing from
>>     binaries) is:
>>
>>     user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion
>>
>>     Scipion v2.0 (2019-04-23) Diocletian
>>
>>     >>>>> python /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
>>
>>     Traceback (most recent call last):
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py",
>>     line 32, in <module>
>>
>>         from pyworkflow.gui.project import ProjectManagerWindow
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py",
>>     line 27, in <module>
>>
>>         from gui import *
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py",
>>     line 29, in <module>
>>
>>         import Tkinter as tk
>>
>>       File
>>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py",
>>     line 6, in <module>
>>
>>         from Tkinter import (_cnfmerge, _default_root, _flatten,
>>
>>     ImportError: cannot import name _cnfmerge
>>
>>
>>
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>     sers">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
>>
>> >
>>
>> ot;Times New Roman",serif;color:windowtext;mso-fareast-language:SV">>
>>
>>
>> _______________________________________________
>> 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*

Re: [scipion-users] Installation problems (WSL)

[Pablo C. <pc...@cn...>]

I guess changes of this (https://github.com/python-zk/kazoo/issues/239) 
being your case are low, but just in case?


On 13/8/19 15:51, Viktor Bengtsson wrote:
>
> Thanks for the suggestion. Unfortunately I get the same error:
>
> /mnt/e/Linux_programs/scipion$ scipion python -m pip install requests
>
> Scipion v2.0 (2019-04-23) Diocletian
>
> >>>>> python  "-m" "pip" "install" "requests"
>
> Traceback (most recent call last):
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
> line 174, in _run_module_as_main
>
> "__main__", fname, loader, pkg_name)
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
> line 72, in _run_code
>
> exec code in run_globals
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", 
> line 16, in <module>
>
> from pip._internal import main as _main  # isort:skip # noqa
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", 
> line 19, in <module>
>
> from pip._vendor.urllib3.exceptions import DependencyWarning
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", 
> line 8, in <module>
>
> from .connectionpool import (
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", 
> line 44, in <module>
>
> from .util.queue import LifoQueue
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", 
> line 7, in <module>
>
> import Queue as _unused_module_Queue  # noqa: F401
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", 
> line 10, in <module>
>
> class LifoQueue(queue.Queue):
>
> AttributeError: 'module' object has no attribute 'Queue'
>
> Kind regards,
>
> Viktor
>
> *From:*Pablo Conesa <pc...@cn...>
> *Sent:* den 13 augusti 2019 14:40
> *To:* sci...@li...
> *Subject:* Re: [scipion-users] Installation problems (WSL)
>
> What if you do:
>
> scipion python -m pip install requests
>
> On 13/8/19 13:18, Viktor Bengtsson wrote:
>
>     Hi,
>
>     I tried what you suggested, but nothing seems to work. All
>     packages installed prior to requests seem to install properly, so
>     I wonder if there is something in particular related to that
>     package that causes an error. Alternatively, is there some
>     workaround to install that package into site-packages without
>     using pip included with the installation of Scipion?
>
>     Kind regards,
>
>     Viktor
>
>     *From:*Lugmayr, Wolfgang <w.l...@uk...> <mailto:w.l...@uk...>
>     *Sent:* den 12 augusti 2019 16:47
>     *To:* Mailing list for Scipion users
>     <sci...@li...>
>     <mailto:sci...@li...>
>     *Subject:* Re: [scipion-users] Installation problems (WSL)
>
>     hi,
>
>     maybe your os python is mixed up with the scipion one:
>
>     can you check the following environment variables and test to set
>     the scipion path first?
>
>     LD_LIBRARY_PATH /whereever.../scipion/software/lib
>     PYTHONPATH /whereever.../scipion/software/lib
>
>     cheers,
>
>     wolfgang
>
>     ------------------------------------------------------------------------
>
>     *From: *"Viktor Bengtsson" <vik...@mm...
>     <mailto:vik...@mm...>>
>     *To: *"Mailing list for Scipion users"
>     <sci...@li...
>     <mailto:sci...@li...>>
>     *Sent: *Monday, 12 August, 2019 14:49:20
>     *Subject: *[scipion-users] Installation problems (WSL)
>
>     Dear all,
>
>     Before summer I could use Scipion without problem. However, after
>     vacation (and possibly some change in environment) it would not
>     start at all. Unfortunately I did not save the error message
>     before trying to reinstall, and reinstallation does not seem to
>     work at all.
>
>     The initial attempt was made on Ubuntu 16.04 installed through WSL
>     on my work computer. I also tried installing on Ubuntu 18.04
>     installed on WSL on my home computer (where I have not used WSL at
>     all previously, so no prior python installation). In all cases
>     there have been a number of problems compiling python packages,
>     and I can’t start Scipion.
>
>     I followed the instructions found at
>     https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install,
>     both for “From Binaries” and “Sources from GitHub”. The attached
>     log files should include all input and all output.
>
>     Does anyone know what might be the problem?
>
>     Kind regards,
>
>     Viktor Bengtsson
>
>     PhD student
>
>     Stockholm University
>
>     PS. The final error I get when attempting to install from sources is :
>
>     /mnt/e/Linux_programs/scipion/scipion/software/bin/python
>     /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>     install requests==2.18.4
>
>     Traceback (most recent call last):
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>     line 174, in _run_module_as_main
>
>         "__main__", fname, loader, pkg_name)
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py",
>     line 72, in _run_code
>
>         exec code in run_globals
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py",
>     line 16, in <module>
>
>         from pip._internal import main as _main  # isort:skip # noqa
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py",
>     line 19, in <module>
>
>         from pip._vendor.urllib3.exceptions import DependencyWarning
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py",
>     line 7, in <module>
>
>         from .connectionpool import (
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py",
>     line 45, in <module>
>
>         from .util.queue import LifoQueue
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py",
>     line 7, in <module>
>
>         import Queue as _unused_module_Queue # noqa: F401
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py",
>     line 10, in <module>
>
>         class LifoQueue(queue.Queue):
>
>     AttributeError: 'module' object has no attribute 'Queue'
>
>     Error: target
>     '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests'
>     not built (after running
>     '/mnt/e/Linux_programs/scipion/scipion/software/bin/python
>     /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip
>     install requests==2.18.4')
>
>     The original error (that reoccurred after installing from
>     binaries) is:
>
>     user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion
>
>     Scipion v2.0 (2019-04-23) Diocletian
>
>     >>>>> python /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
>
>     Traceback (most recent call last):
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py",
>     line 32, in <module>
>
>         from pyworkflow.gui.project import ProjectManagerWindow
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py",
>     line 27, in <module>
>
>         from gui import *
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py",
>     line 29, in <module>
>
>         import Tkinter as tk
>
>       File
>     "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py",
>     line 6, in <module>
>
>         from Tkinter import (_cnfmerge, _default_root, _flatten,
>
>     ImportError: cannot import name _cnfmerge
>
>
>
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>     sers">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
>
> >
>
> ot;Times New Roman",serif;color:windowtext;mso-fareast-language:SV">>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] Installation problems (WSL)

[Viktor B. <vik...@mm...>]

Thanks for the suggestion. Unfortunately I get the same error:

/mnt/e/Linux_programs/scipion$ scipion python -m pip install requests

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  "-m" "pip" "install" "requests"
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 8, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 44, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'

Kind regards,
Viktor

From: Pablo Conesa <pc...@cn...>
Sent: den 13 augusti 2019 14:40
To: sci...@li...
Subject: Re: [scipion-users] Installation problems (WSL)


What if you do:

scipion python -m pip install requests
On 13/8/19 13:18, Viktor Bengtsson wrote:
Hi,
I tried what you suggested, but nothing seems to work. All packages installed prior to requests seem to install properly, so I wonder if there is something in particular related to that package that causes an error. Alternatively, is there some workaround to install that package into site-packages without using pip included with the installation of Scipion?

Kind regards,
Viktor

From: Lugmayr, Wolfgang <w.l...@uk...><mailto:w.l...@uk...>
Sent: den 12 augusti 2019 16:47
To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...>
Subject: Re: [scipion-users] Installation problems (WSL)

hi,

maybe your os python is mixed up with the scipion one:

can you check the following environment variables and test to set the scipion path first?
LD_LIBRARY_PATH /whereever.../scipion/software/lib
PYTHONPATH /whereever.../scipion/software/lib
cheers,
wolfgang


________________________________
From: "Viktor Bengtsson" <vik...@mm...<mailto:vik...@mm...>>
To: "Mailing list for Scipion users" <sci...@li...<mailto:sci...@li...>>
Sent: Monday, 12 August, 2019 14:49:20
Subject: [scipion-users] Installation problems (WSL)

Dear all,
Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all.

The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can’t start Scipion.

I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install<https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install>, both for “From Binaries” and “Sources from GitHub”. The attached log files should include all input and all output.

Does anyone know what might be the problem?

Kind regards,
Viktor Bengtsson
PhD student
Stockholm University

PS. The final error I get when attempting to install from sources is :

/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'
Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4')

The original error (that reoccurred after installing from binaries) is:
user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module>
    import Tkinter as tk
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module>
    from Tkinter import (_cnfmerge, _default_root, _flatten,
ImportError: cannot import name _cnfmerge


_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
sers">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
>
ourceforge.net<mailto:sci...@li...>

https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Installation problems (WSL)

[Pablo C. <pc...@cn...>]

What if you do:

scipion python -m pip install requests

On 13/8/19 13:18, Viktor Bengtsson wrote:
>
> Hi,
>
> I tried what you suggested, but nothing seems to work. All packages 
> installed prior to requests seem to install properly, so I wonder if 
> there is something in particular related to that package that causes 
> an error. Alternatively, is there some workaround to install that 
> package into site-packages without using pip included with the 
> installation of Scipion?
>
> Kind regards,
>
> Viktor
>
> *From:*Lugmayr, Wolfgang <w.l...@uk...>
> *Sent:* den 12 augusti 2019 16:47
> *To:* Mailing list for Scipion users <sci...@li...>
> *Subject:* Re: [scipion-users] Installation problems (WSL)
>
> hi,
>
> maybe your os python is mixed up with the scipion one:
>
> can you check the following environment variables and test to set the 
> scipion path first?
>
> LD_LIBRARY_PATH /whereever.../scipion/software/lib
> PYTHONPATH /whereever.../scipion/software/lib
>
> cheers,
>
> wolfgang
>
> ------------------------------------------------------------------------
>
> *From: *"Viktor Bengtsson" <vik...@mm... 
> <mailto:vik...@mm...>>
> *To: *"Mailing list for Scipion users" 
> <sci...@li... 
> <mailto:sci...@li...>>
> *Sent: *Monday, 12 August, 2019 14:49:20
> *Subject: *[scipion-users] Installation problems (WSL)
>
> Dear all,
>
> Before summer I could use Scipion without problem. However, after 
> vacation (and possibly some change in environment) it would not start 
> at all. Unfortunately I did not save the error message before trying 
> to reinstall, and reinstallation does not seem to work at all.
>
> The initial attempt was made on Ubuntu 16.04 installed through WSL on 
> my work computer. I also tried installing on Ubuntu 18.04 installed on 
> WSL on my home computer (where I have not used WSL at all previously, 
> so no prior python installation). In all cases there have been a 
> number of problems compiling python packages, and I can’t start Scipion.
>
> I followed the instructions found at 
> https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install, 
> both for “From Binaries” and “Sources from GitHub”. The attached log 
> files should include all input and all output.
>
> Does anyone know what might be the problem?
>
> Kind regards,
>
> Viktor Bengtsson
>
> PhD student
>
> Stockholm University
>
> PS. The final error I get when attempting to install from sources is :
>
> /mnt/e/Linux_programs/scipion/scipion/software/bin/python 
> /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip 
> install requests==2.18.4
>
> Traceback (most recent call last):
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
> line 174, in _run_module_as_main
>
> "__main__", fname, loader, pkg_name)
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", 
> line 72, in _run_code
>
> exec code in run_globals
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", 
> line 16, in <module>
>
> from pip._internal import main as _main  # isort:skip # noqa
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", 
> line 19, in <module>
>
> from pip._vendor.urllib3.exceptions import DependencyWarning
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", 
> line 7, in <module>
>
> from .connectionpool import (
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", 
> line 45, in <module>
>
> from .util.queue import LifoQueue
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", 
> line 7, in <module>
>
> import Queue as _unused_module_Queue  # noqa: F401
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", 
> line 10, in <module>
>
> class LifoQueue(queue.Queue):
>
> AttributeError: 'module' object has no attribute 'Queue'
>
> Error: target 
> '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' 
> not built (after running 
> '/mnt/e/Linux_programs/scipion/scipion/software/bin/python 
> /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip 
> install requests==2.18.4')
>
> The original error (that reoccurred after installing from binaries) is:
>
> user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion
>
> Scipion v2.0 (2019-04-23) Diocletian
>
> >>>>> python 
> /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
>
> Traceback (most recent call last):
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", 
> line 32, in <module>
>
> from pyworkflow.gui.project import ProjectManagerWindow
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", 
> line 27, in <module>
>
> from gui import *
>
> File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", 
> line 29, in <module>
>
> import Tkinter as tk
>
> File 
> "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", 
> line 6, in <module>
>
> from Tkinter import (_cnfmerge, _default_root, _flatten,
>
> ImportError: cannot import name _cnfmerge
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li... 
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> sers">https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Installation problems (WSL)

[Viktor B. <vik...@mm...>]

Hi,
I tried what you suggested, but nothing seems to work. All packages installed prior to requests seem to install properly, so I wonder if there is something in particular related to that package that causes an error. Alternatively, is there some workaround to install that package into site-packages without using pip included with the installation of Scipion?

Kind regards,
Viktor

From: Lugmayr, Wolfgang <w.l...@uk...>
Sent: den 12 augusti 2019 16:47
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] Installation problems (WSL)

hi,

maybe your os python is mixed up with the scipion one:

can you check the following environment variables and test to set the scipion path first?
LD_LIBRARY_PATH /whereever.../scipion/software/lib
PYTHONPATH /whereever.../scipion/software/lib
cheers,
wolfgang


________________________________
From: "Viktor Bengtsson" <vik...@mm...<mailto:vik...@mm...>>
To: "Mailing list for Scipion users" <sci...@li...<mailto:sci...@li...>>
Sent: Monday, 12 August, 2019 14:49:20
Subject: [scipion-users] Installation problems (WSL)

Dear all,
Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all.

The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can’t start Scipion.

I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install<https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install>, both for “From Binaries” and “Sources from GitHub”. The attached log files should include all input and all output.

Does anyone know what might be the problem?

Kind regards,
Viktor Bengtsson
PhD student
Stockholm University

PS. The final error I get when attempting to install from sources is :

/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'
Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4')

The original error (that reoccurred after installing from binaries) is:
user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module>
    import Tkinter as tk
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module>
    from Tkinter import (_cnfmerge, _default_root, _flatten,
ImportError: cannot import name _cnfmerge


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Re: [scipion-users] OpenCV not found for Xmipp

[Carlos O. S. S. <co...@cn...>]

Thanks a lot.

El 12/08/2019 a las 18:10, Lugmayr, Wolfgang escribió:
> hi,
>
> i fixed now the problem with opencv and got a running gpu-based xmipp 
> from source (set opencv version in config and put cuda-8.0 into path):
> ./scipion install opencv -j 1
> cd software
> ln -s lib lib64
> cd tmp/opencv-3.4.1
> rm -rf build; mkdir build; cd build
> cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX=/beegfs/cssb/software/em/scipion/2.0/software \
>    -DTIFF_LIBRARY=/beegfs/cssb/software/em/scipion/2.0/software/lib/libtiff.so -DWITH_VTK=NO -DWITH_NVCUVID=NO ..
> make
> make install
> cheers,
> wolfgang
>
> ------------------------------------------------------------------------
> *From: *"Lugmayr, Wolfgang" <w.l...@uk...>
> *To: *"Mailing list for Scipion users" 
> <sci...@li...>
> *Sent: *Thursday, 13 June, 2019 11:22:33
> *Subject: *Re: [scipion-users] OpenCV not found for Xmipp
>
> hi david,
>
> sorry it took a while to try your tip.
>
> now i have a python problem:
> cmake -DWITH_FFMPEG=OFF 
> -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF 
> -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software 
> . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 
> 2>&1
> Error: target 
> '/beegfs/cssb/software/em/scipion/2.0/software/tmp/opencv-2.4.13/Makefile' 
> not built (after running 'cmake -DWITH_FFMPEG=OFF 
> -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF 
> -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software 
> . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 
> 2>&1')
>
> the lines in the log are:
> -- Could NOT find PythonLibs: Found unsuitable version "2.7.5", but 
> required is exact version "2.7.15" (found /lib64/libpython2.7.so)
> :
> --   Python:
> --     Interpreter: 
> /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 (ver 2.7.15)
> --     Libraries:                   /lib64/libpython2.7.so (ver 2.7.5)
> --     numpy: 
> /beegfs/cssb/software/em/scipion/2.0/software/lib/python2.7/site-packages/numpy/core/include 
> (ver 1.14.1)
> --     packages path: lib/python2.7/site-packages
>
> so if i do in a new login terminal:
> $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2
>     libpython2.7.so.1.0 => /lib64/libpython2.7.so.1.0 (0x00002b49812b3000)
>
> i also made an environment module to set the LD_LIBRARY_PATH to the 
> right location and then:
> $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2
>     libpython2.7.so.1.0 => 
> /beegfs/cssb/software/em/scipion/2.0/software/lib/libpython2.7.so.1.0 
> (0x00002afad38b5000)
>
> but the scipion install seems to ignore these LD_LIBRARY_PATH
>
> cheers,
> wolfgang
>
>
>
>
> ------------------------------------------------------------------------
> *From: *"David Maluenda" <dma...@cn...>
> *To: *"Mailing list for Scipion users" 
> <sci...@li...>
> *Sent: *Wednesday, 29 May, 2019 10:40:48
> *Subject: *Re: [scipion-users] OpenCV not found for Xmipp
>
> Hi David, Wolfgang and Scipion users,
>
> Regarding the first question of why the openCV code of Xmipp is not 
> compailing when OpenCV is in a alternate location, Xmipp needs the 
> headers files of OpenCV to compile that part of the code, thus you 
> must have installed the devel version of the OpenCV package and, also, 
> the include folder of the openCV must be seeable during the 
> compilation time.
>
> Regarding the libtiff versions fight, yes Scipion has libtiff5, then 
> if other libtiff is used to compile the system's openCV, it will fail.
>
> Both issues might be fixed by installing OpenCV inside Scipion via
>
> $ cd $SCIPION_HOME
> $ ./scipion install opencv -j N
>
> where N is the number of processors (take into account that this 
> installation takes a while, thus the bigger N is better).
>
> NOTE: Regarding the OpenCV inside Scipion, we have using the 
> OpenCV-v2.4.13 by default and we have checked that it works fine for 
> Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that 
> the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you 
> should edit the$SCIPION_HOME/config/scipion.conf in such a way that 
> OPENCV_VER=3.4.1 and then install opencv using the command above (this 
> only works if Scipion is installed from sources, not from binaries).
>
>
> Finally, just to note that OpenCV is used by Xmipp only for two non 
> critical protocols (Optical Alignment and Enric -former Volume 
> Homogenizer-). Therefore, if you don't need this two protocols and it 
> still not working even with the hints pointed out above, the OpenCV 
> code in Xmipp can be ignored by editing 
> $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, 
> then, trying to compile Xmipp again.
>
>
> I hope tht it will help and my appologies for the late reply.
>
>
> Thanks for reporting!
>
>
> *_____
> Dr. David Maluenda Niubó*
> dma...@cn... <mailto:dma...@cn...> - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
> BioComputing Unit <http://biocomputingunit.es/>
>
> This email message and any documents attached to it may contain 
> confidential or legally protected material and are intended solely for 
> the use of the individual or organization to whom they are addressed. 
> We remind you that if you are not the intended recipient of this email 
> message or the person responsible for processing it, then you are not 
> authorized to read, save, modify, send, copy or disclose any of its 
> contents. If you have received this email message by mistake, we 
> kindly ask you to inform the sender of this and to eliminate both the 
> message and any attachments it carries from your account. Thank you 
> for your collaboration.
>
>
>
> On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via 
> scipion-users <sci...@li... 
> <mailto:sci...@li...>> wrote:
>
>     No.  I've been attempting to compile Xmipp from source, but that
>     is even harder.
>
>     David Hoover
>     HPC @ NIH
>
>     On 5/27/2019 11:28 AM, Pablo Conesa wrote:
>     > Hi David! Have we ever replied to you with a solution?
>     >
>     > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users
>     wrote:
>     >> Hi,
>     >>
>     >> I recently installed Scipion 2.0 and all the plugins, and
>     attempted to run the tutorials.  We have OpenCV installed in an
>     alternate location, and I make it available by setting $PATH and
>     $LD_LIBRARY_PATH.  I keep getting complaints that it is not
>     installed, and that I should fix this and reinstall Xmipp.
>     >>
>     >> How does Xmipp know where OpenCV is?  Can I set a configuration
>     somewhere stating where it is located?
>     >>
>     >> David Hoover
>     >> HPC @ NIH
>     >>
>     >>
>     >> _______________________________________________
>     >> 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
>
>
>
> _______________________________________________
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> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
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> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
------------------------------------------------------------------------

Re: [scipion-users] OpenCV not found for Xmipp

[Lugmayr, W. <w.l...@uk...>]

hi, 

i fixed now the problem with opencv and got a running gpu-based xmipp from source (set opencv version in config and put cuda-8.0 into path): 
./scipion install opencv -j 1
cd software
ln -s lib lib64
cd tmp/opencv-3.4.1
rm -rf build; mkdir build; cd build
cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX=/beegfs/cssb/software/em/scipion/2.0/software \
  -DTIFF_LIBRARY=/beegfs/cssb/software/em/scipion/2.0/software/lib/libtiff.so -DWITH_VTK=NO -DWITH_NVCUVID=NO .. 
make 
make install 
cheers, 
wolfgang 


From: "Lugmayr, Wolfgang" <w.l...@uk...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Thursday, 13 June, 2019 11:22:33 
Subject: Re: [scipion-users] OpenCV not found for Xmipp 

hi david, 

sorry it took a while to try your tip. 

now i have a python problem: 
cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 2>&1 
Error: target '/beegfs/cssb/software/em/scipion/2.0/software/tmp/opencv-2.4.13/Makefile' not built (after running 'cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log 2>&1') 

the lines in the log are: 
-- Could NOT find PythonLibs: Found unsuitable version "2.7.5", but required is exact version "2.7.15" (found /lib64/libpython2.7.so) 
: 
-- Python: 
-- Interpreter: /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 (ver 2.7.15) 
-- Libraries: /lib64/libpython2.7.so (ver 2.7.5) 
-- numpy: /beegfs/cssb/software/em/scipion/2.0/software/lib/python2.7/site-packages/numpy/core/include (ver 1.14.1) 
-- packages path: lib/python2.7/site-packages 

so if i do in a new login terminal: 
$ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 
libpython2.7.so.1.0 => /lib64/libpython2.7.so.1.0 (0x00002b49812b3000) 

i also made an environment module to set the LD_LIBRARY_PATH to the right location and then: 
$ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 
libpython2.7.so.1.0 => /beegfs/cssb/software/em/scipion/2.0/software/lib/libpython2.7.so.1.0 (0x00002afad38b5000) 

but the scipion install seems to ignore these LD_LIBRARY_PATH 

cheers, 
wolfgang 





From: "David Maluenda" <dma...@cn...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Wednesday, 29 May, 2019 10:40:48 
Subject: Re: [scipion-users] OpenCV not found for Xmipp 

Hi David, Wolfgang and Scipion users, 

Regarding the first question of why the openCV code of Xmipp is not compailing when OpenCV is in a alternate location, Xmipp needs the headers files of OpenCV to compile that part of the code, thus you must have installed the devel version of the OpenCV package and, also, the include folder of the openCV must be seeable during the compilation time. 

Regarding the libtiff versions fight, yes Scipion has libtiff5, then if other libtiff is used to compile the system's openCV, it will fail. 

Both issues might be fixed by installing OpenCV inside Scipion via 

$ cd $SCIPION_HOME 
$ ./scipion install opencv -j N 

where N is the number of processors (take into account that this installation takes a while, thus the bigger N is better). 

NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13 by default and we have checked that it works fine for Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you should edit the $SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and then install opencv using the command above (this only works if Scipion is installed from sources, not from binaries). 


Finally, just to note that OpenCV is used by Xmipp only for two non critical protocols (Optical Alignment and Enric -former Volume Homogenizer-). Therefore, if you don't need this two protocols and it still not working even with the hints pointed out above, the OpenCV code in Xmipp can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, then, trying to compile Xmipp again. 


I hope tht it will help and my appologies for the late reply. 


Thanks for reporting! 

[ http://ucm.es/ ] 
_____ 
Dr. David Maluenda Niubó 
[ mailto:dma...@cn... | dma...@cn... ] - (+34) 619 029 310 
[ http://www.cnb.csic.es/ | CSIC - Centro Nacional de Biotecnología ] 
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On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via scipion-users < [ mailto:sci...@li... | sci...@li... ] > wrote: 


No. I've been attempting to compile Xmipp from source, but that is even harder. 

David Hoover 
HPC @ NIH 

On 5/27/2019 11:28 AM, Pablo Conesa wrote: 
> Hi David! Have we ever replied to you with a solution? 
> 
> On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote: 
>> Hi, 
>> 
>> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials. We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH. I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp. 
>> 
>> How does Xmipp know where OpenCV is? Can I set a configuration somewhere stating where it is located? 
>> 
>> David Hoover 
>> HPC @ NIH 
>> 
>> 
>> _______________________________________________ 
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>> [ mailto:sci...@li... | sci...@li... ] 
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> 
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Re: [scipion-users] Installation problems (WSL)

[Lugmayr, W. <w.l...@uk...>]

hi, 

maybe your os python is mixed up with the scipion one: 

can you check the following environment variables and test to set the scipion path first? 
LD_LIBRARY_PATH /whereever.../scipion/software/lib 
PYTHONPATH /whereever.../scipion/software/lib 

cheers, 
wolfgang 



From: "Viktor Bengtsson" <vik...@mm...> 
To: "Mailing list for Scipion users" <sci...@li...> 
Sent: Monday, 12 August, 2019 14:49:20 
Subject: [scipion-users] Installation problems (WSL) 



Dear all, 

Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all. 



The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can’t start Scipion. 



I followed the instructions found at [ https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install | https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install ] , both for “From Binaries” and “Sources from GitHub”. The attached log files should include all input and all output. 



Does anyone know what might be the problem? 



Kind regards, 

Viktor Bengtsson 

PhD student 

Stockholm University 



PS. The final error I get when attempting to install from sources is : 



/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4 

Traceback (most recent call last): 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main 

"__main__", fname, loader, pkg_name) 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code 

exec code in run_globals 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module> 

from pip._internal import main as _main # isort:skip # noqa 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module> 

from pip._vendor.urllib3.exceptions import DependencyWarning 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module> 

from .connectionpool import ( 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module> 

from .util.queue import LifoQueue 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module> 

import Queue as _unused_module_Queue # noqa: F401 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module> 

class LifoQueue(queue.Queue): 

AttributeError: 'module' object has no attribute 'Queue' 

Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4') 



The original error (that reoccurred after installing from binaries) is: 

user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion 



Scipion v2.0 (2019-04-23) Diocletian 



>>>>> python /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py 

Traceback (most recent call last): 

File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module> 

from pyworkflow.gui.project import ProjectManagerWindow 

File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module> 

from gui import * 

File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module> 

import Tkinter as tk 

File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module> 

from Tkinter import (_cnfmerge, _default_root, _flatten, 

ImportError: cannot import name _cnfmerge 


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https://lists.sourceforge.net/lists/listinfo/scipion-users 

[scipion-users] Installation problems (WSL)

[Viktor B. <vik...@mm...>]

Dear all,
Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all.

The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can't start Scipion.

I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install, both for "From Binaries" and "Sources from GitHub". The attached log files should include all input and all output.

Does anyone know what might be the problem?

Kind regards,
Viktor Bengtsson
PhD student
Stockholm University

PS. The final error I get when attempting to install from sources is :

/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'
Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4')

The original error (that reoccurred after installing from binaries) is:
user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module>
    import Tkinter as tk
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module>
    from Tkinter import (_cnfmerge, _default_root, _flatten,
ImportError: cannot import name _cnfmerge

Re: [scipion-users] Region CTF-refinement error

[Dmitry A. S. <sem...@gm...>]

Dear Grigory,


The issue was that I didn't use the auto-refine as an input.

Thank you for you help.

Sincerely,
Dmitry


On August 6, 2019 10:48:23 Gregory Sharov <sha...@gm...> wrote:
> Hi Dmitry,
>
>
> can you check what column is missing in the input star file? Is it 
> rlnRandomSubset? Where do these particles come from?
>
>
> 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
> e-mail: gs...@mr...
>
>
>
>
>
> On Tue, Aug 6, 2019 at 9:26 AM Dmitry Semchonok <sem...@gm...> wrote:
>
> Dear colleagues,
>
>
> The relion CTF-refinement protocol gives an error
>
>
> Please see the screenshots.
>
>
> Sincerely,
> Dmitry
> _______________________________________________
> 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

Re: [scipion-users] Region CTF-refinement error

[Dmitry A. S. <sem...@gm...>]

Dear Jose Miguel,

Thank you very much!

Yes I will do that!

Sincerely,
Dmitry

On August 6, 2019 10:48:23 Jose Miguel de la Rosa Trevin 
<del...@gm...> wrote:
> Dear Dmitry,
>
> Remember that for CTF - refinement, you need to use an input set of 
> particles that contains 3D angular assignment,
> either coming from Relion - 3d autorefine or any other protocol for 3D 
> refinement.
>
> Best,
> Jose Miguel
>
>
>
> On Tue, Aug 6, 2019 at 10:26 AM Dmitry Semchonok <sem...@gm...> wrote:
> Dear colleagues,
>
> The relion CTF-refinement protocol gives an error
>
> Please see the screenshots.
>
>
> Sincerely,
> Dmitry
> _______________________________________________
> 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

Re: [scipion-users] Region CTF-refinement error

[Gregory S. <sha...@gm...>]

Hi Dmitry,

can you check what column is missing in the input star file? Is it
rlnRandomSubset? Where do these particles come from?

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, Aug 6, 2019 at 9:26 AM Dmitry Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> The relion CTF-refinement protocol gives an error
>
> Please see the screenshots.
>
> Sincerely,
> Dmitry
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>