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From: Pablo C. <pc...@cn...> - 2018-07-10 10:01:29
|
is java in your path? what happens if you type in the "console/terminal": java -version On 09/07/18 14:39, David Maluenda wrote: > Ouch.. strange.. > > What appears as Output for the Xmipp-ExtractParticles? Could the > output set be empty? > The summary tab (in the scipion GUI) should display:/// > / > / > / > /Name-of-the-protocol/ -> outputParticles SetOfParticles > (_*# items*_, ** x **, **.* A/px ) > > Then, the number of items # is bigger than 0? > > <http://ucm.es/> > *_____ > 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 Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm... > <mailto:eri...@gm...>> wrote: > > Hi David, > > I am not receiving any error messages from Scipion after the > command. However, there is no new window popping out after the > command. > > Erik Zupa > > > On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda > <dma...@cn... <mailto:dma...@cn...>> wrote: > > Hi Erik, > > This is the command that Scipion launch to open the viewer and > it looks fine.. so, it should open a window with the particles... > > Is there any error message after the command that you are > reporting? > > Thanks! > > <http://ucm.es/> > *_____ > 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 Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm... > <mailto:eri...@gm...>> wrote: > > Hello colleagues, > > > I have problem to analyze results of extracting of > particles. I successfully ran xmipp3- extract particles. > However, I cannot analyze results because everytime I try, > Scipion come with something like this: > > > java -Xmx2g -d64 > -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib > -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins > -cp > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/* > xmipp.viewer.scipion.ScipionViewer -i > "Runs/002809_XmippProtExtractParticles/particles.sqlite" > --visible id enabled _index _filename _xmipp_zScore > _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU > _ctfModel._defocusV _ctfModel._defocusAngle > _transform._matrix --order id enabled _index _filename > _xmipp_zScore _xmipp_cumulativeSSNR _sampling > _ctfModel._defocusU _ctfModel._defocusV > _ctfModel._defocusAngle _transform._matrix --render > _filename --sortby _xmipp_zScore asc --scipion 55971 2856 > > > I am thankful for any help. > > > Erik Zupa > > CEITEC Brno Czech Republic > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's > most > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: David M. <dma...@cn...> - 2018-07-09 12:40:29
|
Ouch.. strange.. What appears as Output for the Xmipp-ExtractParticles? Could the output set be empty? The summary tab (in the scipion GUI) should display: *Name-of-the-protocol* -> outputParticles SetOfParticles (* # items*, ** x **, **.* A/px ) Then, the number of items # is bigger than 0? <http://ucm.es/> *_____Dr. David Maluenda Niubó* 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 Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote: > Hi David, > > I am not receiving any error messages from Scipion after the command. > However, there is no new window popping out after the command. > > Erik Zupa > > > On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...> > wrote: > >> Hi Erik, >> >> This is the command that Scipion launch to open the viewer and it looks >> fine.. so, it should open a window with the particles... >> >> Is there any error message after the command that you are reporting? >> >> Thanks! >> >> <http://ucm.es/> >> >> *_____Dr. David Maluenda Niubó* >> 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 Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote: >> >>> Hello colleagues, >>> >>> >>> I have problem to analyze results of extracting of particles. I >>> successfully ran xmipp3- extract particles. However, I cannot analyze >>> results because everytime I try, Scipion come with something like this: >>> >>> >>> java -Xmx2g -d64 >>> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib >>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins >>> -cp >>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/* >>> xmipp.viewer.scipion.ScipionViewer -i >>> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id >>> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling >>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle >>> _transform._matrix --order id enabled _index _filename _xmipp_zScore >>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV >>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby >>> _xmipp_zScore asc --scipion 55971 2856 >>> >>> >>> I am thankful for any help. >>> >>> Erik Zupa >>> >>> CEITEC Brno Czech Republic >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> > |
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From: Erik Ž. <eri...@gm...> - 2018-07-09 11:23:32
|
Hi David, I am not receiving any error messages from Scipion after the command. However, there is no new window popping out after the command. Erik Zupa On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...> wrote: > Hi Erik, > > This is the command that Scipion launch to open the viewer and it looks > fine.. so, it should open a window with the particles... > > Is there any error message after the command that you are reporting? > > Thanks! > > <http://ucm.es/> > > *_____Dr. David Maluenda Niubó* > 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 Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote: > >> Hello colleagues, >> >> >> I have problem to analyze results of extracting of particles. I >> successfully ran xmipp3- extract particles. However, I cannot analyze >> results because everytime I try, Scipion come with something like this: >> >> >> java -Xmx2g -d64 -Djava.library.path=/home/erikzupa/Downloads/scipion_v1. >> 1_2017-06-14_linux64/scipion/software/em/xmipp/lib >> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017- >> 06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins -cp >> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26. >> x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017- >> 06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/ >> Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/* >> xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_ >> XmippProtExtractParticles/particles.sqlite" --visible id enabled _index >> _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU >> _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix --order id >> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling >> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle >> _transform._matrix --render _filename --sortby _xmipp_zScore asc --scipion >> 55971 2856 >> >> >> I am thankful for any help. >> >> Erik Zupa >> >> CEITEC Brno Czech Republic >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >> _________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > |
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From: David M. <dma...@cn...> - 2018-07-09 10:25:50
|
Hi Erik, This is the command that Scipion launch to open the viewer and it looks fine.. so, it should open a window with the particles... Is there any error message after the command that you are reporting? Thanks! <http://ucm.es/> *_____Dr. David Maluenda Niubó* 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 Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote: > Hello colleagues, > > > I have problem to analyze results of extracting of particles. I > successfully ran xmipp3- extract particles. However, I cannot analyze > results because everytime I try, Scipion come with something like this: > > > java -Xmx2g -d64 > -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib > -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins > -cp > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/* > xmipp.viewer.scipion.ScipionViewer -i > "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id > enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling > _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle > _transform._matrix --order id enabled _index _filename _xmipp_zScore > _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV > _ctfModel._defocusAngle _transform._matrix --render _filename --sortby > _xmipp_zScore asc --scipion 55971 2856 > > > I am thankful for any help. > > Erik Zupa > > CEITEC Brno Czech Republic > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Erik Ž. <eri...@gm...> - 2018-07-09 09:39:55
|
Hello colleagues, I have problem to analyze results of extracting of particles. I successfully ran xmipp3- extract particles. However, I cannot analyze results because everytime I try, Scipion come with something like this: java -Xmx2g -d64 -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins -cp /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/* xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix --order id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle _transform._matrix --render _filename --sortby _xmipp_zScore asc --scipion 55971 2856 I am thankful for any help. Erik Zupa CEITEC Brno Czech Republic |
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From: David M. B. <Dav...@ut...> - 2018-07-03 15:15:03
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Dustin, My core laboratory could do this. Our fee would be $54/hour. David ======================================= David M. Belnap Electron Microscopy Core Laboratory Department of Biochemistry Department of Biology 2501 SMBB University of Utah Salt Lake City, Utah 84112 USA Phone 801.585.1242 FAX 801.587.3077 Dav...@ut...<mailto:Dav...@ut...> ======================================= On Jun 29, 2018, at 4:59 PM, Dustin Armstrong <Dus...@Va...<mailto:Dus...@Va...>> wrote: Hi, I have EM images (2500x) of tissue sections slides that I would like analyzed; ideally, using a program to highlight and quantify all the homogenize black spherical particles in the images. Is there a place I can outsource or gain (fee-for-service) assistance for this project? thanks, -Dustin Dustin Armstrong, PhD Chief Scientific Officer Valerion Therapeutics www.valerion.com<http://www.valerion.com/> <0202SG-E7584-A_3000X_0004.tiff>------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2018-07-03 09:37:59
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Is this of any help?: https://www.youtube.com/watch?v=LAwe9DroypI&t=156s to start scipion type in the console: ./scipion (assuming you are in the scipion installation folder) On 03/07/18 10:22, JESUS BALTANAS COPADO wrote: > > Hi Pablo, > > Thank you for your response, > We have the fortran libraries in our system. Now, the issue is that we > dont know how to execute the program, we have the mrc. files and > everything is allegedly all set to start but dont know what > instructions should be introduced in the console in order to open our > files and start Scipion > > Thanks again > > Cheers > > > Quoting Pablo Conesa <pc...@cn... <mailto:pc...@cn...>>: > >> Jesus, >> >> seems to be related with a missing fortran library. >> >> Not sure, but I'd try this whole command, just in case you never run it: >> >> sudo apt-get install gcc g++ cmake openjdk-8-jdk libxft-dev >> libssl-dev libxext-dev libxml2-dev libreadline6 libquadmath0 >> libxslt1-dev libopenmpi-dev openmpi-bin libxss-dev libgsl0-dev >> libx11-dev gfortran libfreetype6-dev >> >> From here: >> https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies >> >> >> On 02/07/18 10:39, JESUS BALTANAS COPADO wrote: >>> Dear all, >>> >>> I downloaded the program Scipion in order to open the mrc. files I >>> got from the Polara microscope a couple of weeks ago. We have the >>> following doubt, once we installed Scipion, it appeared the next >>> error, we dont know what instructions we have to introduce in the >>> Ubunto console so we can start Scipion in our computer, please find >>> enclosed a couple of pictures below with the messages that pop up in >>> the console: >>> >>> >>> Thank you very much in advance >>> >>> Cheers >>> Jesús. >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> > > > Jesús. |
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From: JESUS B. C. <jes...@um...> - 2018-07-03 08:22:54
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Hi Pablo, Thank you for your response, We have the fortran libraries in our system. Now, the issue is that we dont know how to execute the program, we have the mrc. files and everything is allegedly all set to start but dont know what instructions should be introduced in the console in order to open our files and start Scipion Thanks again Cheers Quoting Pablo Conesa <pc...@cn...>: > Jesus, > > seems to be related with a missing fortran library. > > Not sure, but I'd try this whole command, just in case you never run it: > > sudo apt-get install gcc g++ cmake openjdk-8-jdk libxft-dev libssl-dev > libxext-dev libxml2-dev libreadline6 libquadmath0 libxslt1-dev > libopenmpi-dev openmpi-bin libxss-dev libgsl0-dev libx11-dev gfortran > libfreetype6-dev > > From here: > https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies > > > On 02/07/18 10:39, JESUS BALTANAS COPADO wrote: > >> Dear all, >> >> I downloaded the program Scipion in order to open the mrc. files I got >> from the Polara microscope a couple of weeks ago. We have the following >> doubt, once we installed Scipion, it appeared the next error, we dont >> know what instructions we have to introduce in the Ubunto console so we >> can start Scipion in our computer, please find enclosed a couple of >> pictures below with the messages that pop up in the console: >> >> Thank you very much in advance >> >> Cheers >> Jesús. >> >> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot >> >> _______________________________________________ scipion-users mailing >> list >> sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users Jesús. |
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From: Pablo C. <pc...@cn...> - 2018-07-03 07:02:46
|
Jesus, seems to be related with a missing fortran library. Not sure, but I'd try this whole command, just in case you never run it: sudo apt-get install gcc g++ cmake openjdk-8-jdk libxft-dev libssl-dev libxext-dev libxml2-dev libreadline6 libquadmath0 libxslt1-dev libopenmpi-dev openmpi-bin libxss-dev libgsl0-dev libx11-dev gfortran libfreetype6-dev From here: https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies On 02/07/18 10:39, JESUS BALTANAS COPADO wrote: > Dear all, > > I downloaded the program Scipion in order to open the mrc. files I got > from the Polara microscope a couple of weeks ago. We have the > following doubt, once we installed Scipion, it appeared the next > error, we dont know what instructions we have to introduce in the > Ubunto console so we can start Scipion in our computer, please find > enclosed a couple of pictures below with the messages that pop up in > the console: > > > Thank you very much in advance > > Cheers > Jesús. > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Pablo C. <pc...@cn...> - 2018-07-03 06:50:55
|
Dear all! Don't know much about this error. It catch my attention the Warning about running mpi as root!!! First time I see it, although it seems to me that is just a warning. Best thing to do is to post this at sci...@li... You can subscribe here: https://sourceforge.net/projects/scipion/lists/scipion-users On 02/07/18 09:37, Carlos Oscar Sorzano wrote: > > Dear Arek, > > > I have not seen this error before, and actually in the log there is no > obvious error. There is a severe warning against running mpi as root > (is it possible that you are running Scipion as root?), but in itself > that should not stop the program. I would try running as a different user. > > > Cheers, Carlos Oscar > > > > -------- Forwarded Message -------- > Subject: Re: Invitation to speak at the 2019 Interdisciplinary > Workshop on single-particle cryo-EM at Rutgers University > Date: Fri, 29 Jun 2018 17:13:33 +0000 > From: Arkadiusz Kulczyk <are...@ru...> > To: Carlos Oscar Sorzano <co...@cn...> > > > > Hi Carlos, > > These are great news! I'm in the process of putting the program > together, so I will follow up with more details shortly. > > If you don't mind I'll use this opportunity to ask the following: I'm > having issues with: relion -3D auto-refine while running it from > Scipion. Wouldn't you mind to have a quick look at the attachment > (run.stdout) and let me know what I'm doing wrong? Many thanks! > > I look forward to welcoming you at Rutgers. > > > Best, > > Arek > > ------------------------------------------------------------------------ > *From:* Carlos Oscar Sorzano <co...@cn...> > *Sent:* Friday, June 29, 2018 12:31:11 PM > *To:* Arkadiusz Kulczyk > *Subject:* Re: Invitation to speak at the 2019 Interdisciplinary > Workshop on single-particle cryo-EM at Rutgers University > > Dear Arek, > > > good to know from you. It will be a pleasure to attend the Workshop. > Is there any particular topic you would be interested and that I could > explain? If not, we are currently working on several topics like > sharpening and volume correction, stream processing, directional > resolution, or continuous heterogeneity. > > > Cheers, Carlos Oscar > > > On 06/26/18 20:02, Arkadiusz Kulczyk wrote: >> >> Dear Carlos, >> >> >> It is with great pleasure that I invite you to be our guest >> speaker at the 6th Interdisciplinary Quantitative Biology Workshop on >> single-particle cryo-EM, which will be held on January 8-12, 2019 at >> Rutgers University. Your presence would be greatly appreciated and >> would provide an inspiration to our young, but rapidly growing >> cryo-EM community at Rutgers. >> >> >> Our facility located in the Institute for Quantitative Biomedicine >> (IQB) was established in 2016, a year prior I joined Rutgers, and it >> houses 200 kV Talos Arctica equipped with a Volta phase plate, an >> energy filter and a K2 direct detector. The IQB is also the >> headquarters of the PDB. I expect that 50-60 participants from >> academia and industry will join the workshop. The plan will include >> morning presentations from invited speakers and practical sessions on >> data collection and image processing in the afternoons. In January >> 2018, we organized a successful workshop on cryo-ET: >> (https://iqb.rutgers.edu/node/90). We would be very honored if you >> decide to participate in the workshop. >> >> >> With best wishes, >> >> Arek >> >> __________________________ >> *Arek Kulczyk, M.Sc., Ph.D.* >> >> Assistant Professor in Biochemistry & Microbiology >> >> & Full Member of Cancer Institute of New Jersey >> >> Institute for Quantitative Biomedicine, Room 208H >> >> Rutgers University >> >> 174 Frelinghuysen Road, Piscataway, NJ 08854, USA >> >> +1 (848) 445-4553 / kulczyk-lab.cryoemcorp.com >> > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail:co...@cn... <mailto:co...@cn...> > Biocomputing unithttp://i2pc.es/coss > <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fi2pc.es%2Fcoss&data=02%7C01%7Carek.kulczyk%40rutgers.edu%7C13a636fb47d44c2285a608d5ddddbcce%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636658866827259962&sdata=%2FQgp%2FSTIpaVDbAidTqyozAari8RBG4UMw8t1vCQWdXM%3D&reserved=0> > 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 > ------------------------------------------------------------------------ |
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From: Kyle D. <kyl...@ep...> - 2018-07-03 06:45:46
|
Hi Jesús, On 07/02/2018 10:39 AM, JESUS BALTANAS COPADO wrote: > Dear all, > > I downloaded the program Scipion in order to open the mrc. files I got > from the Polara microscope a couple of weeks ago. We have the > following doubt, once we installed Scipion, it appeared the next > error, we dont know what instructions we have to introduce in the > Ubunto console so we can start Scipion in our computer Try running the following command to install the Fortran library on your system: sudo apt-get install libgfortran3 Reference: https://askubuntu.com/questions/48117/how-to-install-gfortran Cheers, Kyle -- Kyle M. Douglass, PhD Post-doctoral researcher The Laboratory of Experimental Biophysics EPFL, Lausanne, Switzerland http://kmdouglass.github.io http://leb.epfl.ch |
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From: JESUS B. C. <jes...@um...> - 2018-07-02 08:39:18
|
Dear all, I downloaded the program Scipion in order to open the mrc. files I got from the Polara microscope a couple of weeks ago. We have the following doubt, once we installed Scipion, it appeared the next error, we dont know what instructions we have to introduce in the Ubunto console so we can start Scipion in our computer, please find enclosed a couple of pictures below with the messages that pop up in the console: Thank you very much in advance Cheers Jesús. |
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From: Dustin A. <Dus...@Va...> - 2018-06-30 00:31:54
|
Hi, I have EM images (2500x) of tissue sections slides that I would like analyzed; ideally, using a program to highlight and quantify all the homogenize black spherical particles in the images. Is there a place I can outsource or gain (fee-for-service) assistance for this project? thanks, -Dustin Dustin Armstrong, PhD Chief Scientific Officer Valerion Therapeutics www.valerion.com<http://www.valerion.com> |
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From: Pablo C. <pc...@cn...> - 2018-06-29 06:15:16
|
Thanks Andrew! Your I confirm that --update will not touch already existing values at your ~/.config/scipion/scipion.conf. Sometimes, if your config does not have any special setup, like pointing to other relion installation (e.g.)...it may worth to: 1.- mv ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.backup20180629 2.- scipion config A clean scipion config will point to the latest versions of the em packages. If you have custom CUDA configurations there for some of the packages you will loose them...thus the "backup" Otherwise follow Andrew's instructions. On 27/06/18 14:34, Andrew Purkiss wrote: > > Hi Teige, > > > You need to run > > > scipion config --compare > > > to check for differences in your config file compared to the template > for the scipion version that you are using. > > > scipion config --update > > > should update missing items in the local config, but I don't think it > will change the existing package version. For this you need to edit > ~/.config/scipion/scipion.conf manually to change the package names. > > > Andy > > ------------------------------------------------------------------------ > *From:* Matthews-Palmer, Teige Rowan Seal > <t.m...@im...> > *Sent:* 27 June 2018 13:23:23 > *To:* sci...@li... > *Subject:* [scipion-users] Scipion 1.2 not using installed latest > versions of em packages > Dear Scipion Users, > > I have the following issue with my v1.2 installation: > I installed only the latest versions of packages like motioncor2 & > ctffind4, using scipion install. > When I try to run their protocols, I get an error message that the > binaries for the previous version are missing - it is expecting an > older version than the most up-to-date available to install via > Scipion’s installer. > Any ideas why I might be having this problem and how I can get it to > use the latest versions? > > Thanks a lot, > Teige > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > 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 > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Bruno M. <bru...@gm...> - 2018-06-28 19:20:55
|
Grigory, I tried what you recommended but still the same error message. Pablo, I have python3, how can I try to use it in the installation. Thank you all for the helpful tips. On Thu, 28 Jun 2018 at 15:39, Pablo Conesa <pc...@cn...> wrote: > Not sure, but in this thread someone is blaming the python installation > > https://mail.python.org/pipermail/python-list/2009-April/533221.html > > One option could be to use python3 to kickoff the installation. Do you > have python3 installed? > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Pablo C. <pc...@cn...> - 2018-06-28 19:14:23
|
<div dir='auto'>Can you post the output of the command:<div dir="auto"><br></div><div dir="auto">scipion config</div><div dir="auto"><br></div><div dir="auto"><br></div></div> |
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From: Pablo C. <pc...@cn...> - 2018-06-28 18:39:45
|
<div dir='auto'>Not sure, but in this thread someone is blaming the python installation<div dir="auto"><br></div><div dir="auto">https://mail.python.org/pipermail/python-list/2009-April/533221.html<br></div><div dir="auto"><br></div><div dir="auto">One option could be to use python3 to kickoff the installation. Do you have python3 installed?</div></div> |
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From: Bruno M. <bru...@gm...> - 2018-06-28 17:05:19
|
Sorry Grigory, now I undestand what you were trying to say. So I changed
the scipion file and now the following message is appearing:
bruno@Matsuyama:~/Downloads/scipion$ ./scipion config
Scipion v1.1 (2017-06-14) Balbino
>>>>> python /home/bruno/Downloads/scipion/pyworkflow/apps/pw_config.py
Traceback (most recent call last):
File "/home/bruno/Downloads/scipion/pyworkflow/apps/pw_config.py", line
31, in <module>
import time
ImportError: No module named time
I am just trying to configure the binaries files, in order to install
scipion.
Best Regards,
Bruno
On Thu, 28 Jun 2018 at 13:46, Gregory Sharov <sha...@gm...>
wrote:
> Hi Bruno,
>
> it does look like you still using system python
> (/usr/lib/python2.7/subprocess.py) and not the scipion one. How do you
> launch scipion?
>
> 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 267542
> e-mail: gs...@mr...
>
>
> On Thu, Jun 28, 2018 at 1:48 PM Bruno Matsuyama <bru...@gm...>
> wrote:
>
>> Hi Gregory,
>>
>> I just tried that, but didn't work. The same error message keeps
>> appearing.
>>
>> Traceback (most recent call last):
>> File "./scipion", line 34, in <module>
>> import subprocess
>> File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
>> import select
>> ImportError: No module named select
>>
>> Best Regards,
>>
>> Bruno
>>
>>
>>
>> On Tue, 26 Jun 2018 at 18:48, Gregory Sharov <sha...@gm...>
>> wrote:
>>
>>> Hello Bruno,
>>>
>>> I might be wrong, but a wild guess:do you have anything sourced like
>>> eman2 which might setting its own PYTHONPATH?
>>> Did you try to change first line in the main ./scipion file to point it
>>> to the python provided with scipion? (software/bin/python)
>>>
>>>
>>> On Tue, Jun 26, 2018, 20:01 Bruno Matsuyama <bru...@gm...>
>>> wrote:
>>>
>>>> I searched on the internet and tried some things, but still not work.
>>>> What I found is differences between how the modules are called in the
>>>> script, but I am not sure if I am worsening the situation, because I dont
>>>> have much experience with ubuntu os.
>>>>
>>>> Best Regards,
>>>>
>>>> Bruno
>>>>
>>>> On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...>
>>>> wrote:
>>>>
>>>>> The default python on Ubuntu 18.04 seems to still be 2.7:
>>>>>
>>>>> cnsit@rossmann:/usr/bin$ cat /etc/lsb-release
>>>>> DISTRIB_ID=Ubuntu
>>>>> DISTRIB_RELEASE=18.04
>>>>> DISTRIB_CODENAME=bionic
>>>>> DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS"
>>>>> cnsit@rossmann:/usr/bin$ ls -l python
>>>>> lrwxrwxrwx 1 root root 9 May 8 12:15 python -> python2.7
>>>>>
>>>>>
>>>>> On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote:
>>>>> > Hi Bruno,
>>>>> >
>>>>> > Maybe Ubuntu 18 comes with Python 3 by default? Although we have
>>>>> tested
>>>>> > the install with it.
>>>>> > Did you search about this error in Ubuntu? Just in case could give
>>>>> us
>>>>> > some hint.
>>>>> >
>>>>> > Best,
>>>>> > Jose Miguel
>>>>> >
>>>>> >
>>>>> > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama
>>>>> > <bru...@gm... <mailto:bru...@gm...>> wrote:
>>>>> >
>>>>> > Hello,
>>>>> >
>>>>> > I'm having some trouble to install scipion and I hope that
>>>>> somebody
>>>>> > here can help me. I'm using Ubuntu 18.04, and after installing
>>>>> the
>>>>> > dependencies, when I tried to generate the configuration files, I
>>>>> > get the following message:
>>>>> >
>>>>> > ./scipion config
>>>>> >
>>>>> > Traceback (most recent call last):
>>>>> > File "./scipion", line 34, in <module>
>>>>> > import subprocess
>>>>> > File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
>>>>> > import select
>>>>> > ImportError: No module named select
>>>>> >
>>>>> > Did someone had the same error or know how to fix it ?
>>>>> >
>>>>> > Best Regards,
>>>>> >
>>>>> > Bruno
>>>>> >
>>>>> >
>>>>> ------------------------------------------------------------------------------
>>>>> > Check out the vibrant tech community on one of the world's most
>>>>> > engaging tech sites, Slashdot.org!
>>>>> >
>>>>> http://sdm.link/slashdot_______________________________________________
>>>>> > scipion-users mailing list
>>>>> > sci...@li...
>>>>> > <mailto:sci...@li...>
>>>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>> ------------------------------------------------------------------------------
>>>>> > Check out the vibrant tech community on one of the world's most
>>>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> >
>>>>> >
>>>>> >
>>>>> > _______________________________________________
>>>>> > scipion-users mailing list
>>>>> > sci...@li...
>>>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>> >
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Gregory S. <sha...@gm...> - 2018-06-28 16:46:43
|
Hi Bruno, it does look like you still using system python (/usr/lib/python2.7/subprocess.py) and not the scipion one. How do you launch scipion? 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 267542 e-mail: gs...@mr... On Thu, Jun 28, 2018 at 1:48 PM Bruno Matsuyama <bru...@gm...> wrote: > Hi Gregory, > > I just tried that, but didn't work. The same error message keeps appearing. > > Traceback (most recent call last): > File "./scipion", line 34, in <module> > import subprocess > File "/usr/lib/python2.7/subprocess.py", line 72, in <module> > import select > ImportError: No module named select > > Best Regards, > > Bruno > > > > On Tue, 26 Jun 2018 at 18:48, Gregory Sharov <sha...@gm...> > wrote: > >> Hello Bruno, >> >> I might be wrong, but a wild guess:do you have anything sourced like >> eman2 which might setting its own PYTHONPATH? >> Did you try to change first line in the main ./scipion file to point it >> to the python provided with scipion? (software/bin/python) >> >> >> On Tue, Jun 26, 2018, 20:01 Bruno Matsuyama <bru...@gm...> >> wrote: >> >>> I searched on the internet and tried some things, but still not work. >>> What I found is differences between how the modules are called in the >>> script, but I am not sure if I am worsening the situation, because I dont >>> have much experience with ubuntu os. >>> >>> Best Regards, >>> >>> Bruno >>> >>> On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...> >>> wrote: >>> >>>> The default python on Ubuntu 18.04 seems to still be 2.7: >>>> >>>> cnsit@rossmann:/usr/bin$ cat /etc/lsb-release >>>> DISTRIB_ID=Ubuntu >>>> DISTRIB_RELEASE=18.04 >>>> DISTRIB_CODENAME=bionic >>>> DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS" >>>> cnsit@rossmann:/usr/bin$ ls -l python >>>> lrwxrwxrwx 1 root root 9 May 8 12:15 python -> python2.7 >>>> >>>> >>>> On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote: >>>> > Hi Bruno, >>>> > >>>> > Maybe Ubuntu 18 comes with Python 3 by default? Although we have >>>> tested >>>> > the install with it. >>>> > Did you search about this error in Ubuntu? Just in case could give us >>>> > some hint. >>>> > >>>> > Best, >>>> > Jose Miguel >>>> > >>>> > >>>> > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama >>>> > <bru...@gm... <mailto:bru...@gm...>> wrote: >>>> > >>>> > Hello, >>>> > >>>> > I'm having some trouble to install scipion and I hope that >>>> somebody >>>> > here can help me. I'm using Ubuntu 18.04, and after installing the >>>> > dependencies, when I tried to generate the configuration files, I >>>> > get the following message: >>>> > >>>> > ./scipion config >>>> > >>>> > Traceback (most recent call last): >>>> > File "./scipion", line 34, in <module> >>>> > import subprocess >>>> > File "/usr/lib/python2.7/subprocess.py", line 72, in <module> >>>> > import select >>>> > ImportError: No module named select >>>> > >>>> > Did someone had the same error or know how to fix it ? >>>> > >>>> > Best Regards, >>>> > >>>> > Bruno >>>> > >>>> > >>>> ------------------------------------------------------------------------------ >>>> > Check out the vibrant tech community on one of the world's most >>>> > engaging tech sites, Slashdot.org! >>>> > >>>> http://sdm.link/slashdot_______________________________________________ >>>> > scipion-users mailing list >>>> > sci...@li... >>>> > <mailto:sci...@li...> >>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> > >>>> > >>>> > >>>> > >>>> ------------------------------------------------------------------------------ >>>> > Check out the vibrant tech community on one of the world's most >>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> > >>>> > >>>> > >>>> > _______________________________________________ >>>> > scipion-users mailing list >>>> > sci...@li... >>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> > >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Bruno M. <bru...@gm...> - 2018-06-28 12:48:28
|
Hi Gregory,
I just tried that, but didn't work. The same error message keeps appearing.
Traceback (most recent call last):
File "./scipion", line 34, in <module>
import subprocess
File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
import select
ImportError: No module named select
Best Regards,
Bruno
On Tue, 26 Jun 2018 at 18:48, Gregory Sharov <sha...@gm...>
wrote:
> Hello Bruno,
>
> I might be wrong, but a wild guess:do you have anything sourced like eman2
> which might setting its own PYTHONPATH?
> Did you try to change first line in the main ./scipion file to point it
> to the python provided with scipion? (software/bin/python)
>
>
> On Tue, Jun 26, 2018, 20:01 Bruno Matsuyama <bru...@gm...>
> wrote:
>
>> I searched on the internet and tried some things, but still not work.
>> What I found is differences between how the modules are called in the
>> script, but I am not sure if I am worsening the situation, because I dont
>> have much experience with ubuntu os.
>>
>> Best Regards,
>>
>> Bruno
>>
>> On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...>
>> wrote:
>>
>>> The default python on Ubuntu 18.04 seems to still be 2.7:
>>>
>>> cnsit@rossmann:/usr/bin$ cat /etc/lsb-release
>>> DISTRIB_ID=Ubuntu
>>> DISTRIB_RELEASE=18.04
>>> DISTRIB_CODENAME=bionic
>>> DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS"
>>> cnsit@rossmann:/usr/bin$ ls -l python
>>> lrwxrwxrwx 1 root root 9 May 8 12:15 python -> python2.7
>>>
>>>
>>> On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote:
>>> > Hi Bruno,
>>> >
>>> > Maybe Ubuntu 18 comes with Python 3 by default? Although we have
>>> tested
>>> > the install with it.
>>> > Did you search about this error in Ubuntu? Just in case could give us
>>> > some hint.
>>> >
>>> > Best,
>>> > Jose Miguel
>>> >
>>> >
>>> > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama
>>> > <bru...@gm... <mailto:bru...@gm...>> wrote:
>>> >
>>> > Hello,
>>> >
>>> > I'm having some trouble to install scipion and I hope that
>>> somebody
>>> > here can help me. I'm using Ubuntu 18.04, and after installing the
>>> > dependencies, when I tried to generate the configuration files, I
>>> > get the following message:
>>> >
>>> > ./scipion config
>>> >
>>> > Traceback (most recent call last):
>>> > File "./scipion", line 34, in <module>
>>> > import subprocess
>>> > File "/usr/lib/python2.7/subprocess.py", line 72, in <module>
>>> > import select
>>> > ImportError: No module named select
>>> >
>>> > Did someone had the same error or know how to fix it ?
>>> >
>>> > Best Regards,
>>> >
>>> > Bruno
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > Check out the vibrant tech community on one of the world's most
>>> > engaging tech sites, Slashdot.org!
>>> >
>>> http://sdm.link/slashdot_______________________________________________
>>> > scipion-users mailing list
>>> > sci...@li...
>>> > <mailto:sci...@li...>
>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>>> >
>>> >
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > Check out the vibrant tech community on one of the world's most
>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>> >
>>> >
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>>> > scipion-users mailing list
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>>> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>>> >
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
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From: Jose M. de la R. T. <del...@gm...> - 2018-06-27 12:39:19
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Hi Teige, Andy is right, you need to manually update the package versions in your configuration file (the one under .config in your home pointed by Andy) Best, Jose Miguel On Wed, Jun 27, 2018 at 2:35 PM Andrew Purkiss <And...@cr...> wrote: > Hi Teige, > > > You need to run > > > scipion config --compare > > > to check for differences in your config file compared to the template for > the scipion version that you are using. > > > scipion config --update > > > should update missing items in the local config, but I don't think it will > change the existing package version. For this you need to edit ~/.config/scipion/scipion.conf > manually to change the package names. > > > Andy > > ------------------------------ > *From:* Matthews-Palmer, Teige Rowan Seal < > t.m...@im...> > *Sent:* 27 June 2018 13:23:23 > *To:* sci...@li... > *Subject:* [scipion-users] Scipion 1.2 not using installed latest > versions of em packages > > Dear Scipion Users, > > I have the following issue with my v1.2 installation: > I installed only the latest versions of packages like motioncor2 & > ctffind4, using scipion install. > When I try to run their protocols, I get an error message that the > binaries for the previous version are missing - it is expecting an older > version than the most up-to-date available to install via Scipion’s > installer. > Any ideas why I might be having this problem and how I can get it to use > the latest versions? > > Thanks a lot, > Teige > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > 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 > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Andrew P. <And...@cr...> - 2018-06-27 12:34:57
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Hi Teige, You need to run scipion config --compare to check for differences in your config file compared to the template for the scipion version that you are using. scipion config --update should update missing items in the local config, but I don't think it will change the existing package version. For this you need to edit ~/.config/scipion/scipion.conf manually to change the package names. Andy ________________________________ From: Matthews-Palmer, Teige Rowan Seal <t.m...@im...> Sent: 27 June 2018 13:23:23 To: sci...@li... Subject: [scipion-users] Scipion 1.2 not using installed latest versions of em packages Dear Scipion Users, I have the following issue with my v1.2 installation: I installed only the latest versions of packages like motioncor2 & ctffind4, using scipion install. When I try to run their protocols, I get an error message that the binaries for the previous version are missing - it is expecting an older version than the most up-to-date available to install via Scipion’s installer. Any ideas why I might be having this problem and how I can get it to use the latest versions? Thanks a lot, Teige ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users 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 |
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From: Matthews-Palmer, T. R. S. <t.m...@im...> - 2018-06-27 12:23:36
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Dear Scipion Users, I have the following issue with my v1.2 installation: I installed only the latest versions of packages like motioncor2 & ctffind4, using scipion install. When I try to run their protocols, I get an error message that the binaries for the previous version are missing - it is expecting an older version than the most up-to-date available to install via Scipion’s installer. Any ideas why I might be having this problem and how I can get it to use the latest versions? Thanks a lot, Teige |
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From: Gregory S. <sha...@gm...> - 2018-06-26 21:48:45
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Hello Bruno, I might be wrong, but a wild guess:do you have anything sourced like eman2 which might setting its own PYTHONPATH? Did you try to change first line in the main ./scipion file to point it to the python provided with scipion? (software/bin/python) On Tue, Jun 26, 2018, 20:01 Bruno Matsuyama <bru...@gm...> wrote: > I searched on the internet and tried some things, but still not work. What > I found is differences between how the modules are called in the script, > but I am not sure if I am worsening the situation, because I dont have much > experience with ubuntu os. > > Best Regards, > > Bruno > > On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...> > wrote: > >> The default python on Ubuntu 18.04 seems to still be 2.7: >> >> cnsit@rossmann:/usr/bin$ cat /etc/lsb-release >> DISTRIB_ID=Ubuntu >> DISTRIB_RELEASE=18.04 >> DISTRIB_CODENAME=bionic >> DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS" >> cnsit@rossmann:/usr/bin$ ls -l python >> lrwxrwxrwx 1 root root 9 May 8 12:15 python -> python2.7 >> >> >> On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote: >> > Hi Bruno, >> > >> > Maybe Ubuntu 18 comes with Python 3 by default? Although we have tested >> > the install with it. >> > Did you search about this error in Ubuntu? Just in case could give us >> > some hint. >> > >> > Best, >> > Jose Miguel >> > >> > >> > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama >> > <bru...@gm... <mailto:bru...@gm...>> wrote: >> > >> > Hello, >> > >> > I'm having some trouble to install scipion and I hope that somebody >> > here can help me. I'm using Ubuntu 18.04, and after installing the >> > dependencies, when I tried to generate the configuration files, I >> > get the following message: >> > >> > ./scipion config >> > >> > Traceback (most recent call last): >> > File "./scipion", line 34, in <module> >> > import subprocess >> > File "/usr/lib/python2.7/subprocess.py", line 72, in <module> >> > import select >> > ImportError: No module named select >> > >> > Did someone had the same error or know how to fix it ? >> > >> > Best Regards, >> > >> > Bruno >> > >> > >> ------------------------------------------------------------------------------ >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! >> > >> http://sdm.link/slashdot_______________________________________________ >> > scipion-users mailing list >> > sci...@li... >> > <mailto:sci...@li...> >> > https://lists.sourceforge.net/lists/listinfo/scipion-users >> > >> > >> > >> > >> ------------------------------------------------------------------------------ >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > >> > >> > >> > _______________________________________________ >> > scipion-users mailing list >> > sci...@li... >> > https://lists.sourceforge.net/lists/listinfo/scipion-users >> > >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Bruno M. <bru...@gm...> - 2018-06-26 18:01:10
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I searched on the internet and tried some things, but still not work. What I found is differences between how the modules are called in the script, but I am not sure if I am worsening the situation, because I dont have much experience with ubuntu os. Best Regards, Bruno On Tue, 26 Jun 2018 at 14:56, Patrick Goetz <pg...@ma...> wrote: > The default python on Ubuntu 18.04 seems to still be 2.7: > > cnsit@rossmann:/usr/bin$ cat /etc/lsb-release > DISTRIB_ID=Ubuntu > DISTRIB_RELEASE=18.04 > DISTRIB_CODENAME=bionic > DISTRIB_DESCRIPTION="Ubuntu 18.04 LTS" > cnsit@rossmann:/usr/bin$ ls -l python > lrwxrwxrwx 1 root root 9 May 8 12:15 python -> python2.7 > > > On 06/25/2018 05:44 PM, Jose Miguel de la Rosa Trevin wrote: > > Hi Bruno, > > > > Maybe Ubuntu 18 comes with Python 3 by default? Although we have tested > > the install with it. > > Did you search about this error in Ubuntu? Just in case could give us > > some hint. > > > > Best, > > Jose Miguel > > > > > > On Mon, Jun 25, 2018 at 10:04 PM Bruno Matsuyama > > <bru...@gm... <mailto:bru...@gm...>> wrote: > > > > Hello, > > > > I'm having some trouble to install scipion and I hope that somebody > > here can help me. I'm using Ubuntu 18.04, and after installing the > > dependencies, when I tried to generate the configuration files, I > > get the following message: > > > > ./scipion config > > > > Traceback (most recent call last): > > File "./scipion", line 34, in <module> > > import subprocess > > File "/usr/lib/python2.7/subprocess.py", line 72, in <module> > > import select > > ImportError: No module named select > > > > Did someone had the same error or know how to fix it ? > > > > Best Regards, > > > > Bruno > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! > > > http://sdm.link/slashdot_______________________________________________ > > scipion-users mailing list > > sci...@li... > > <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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