search

jkuharev / ISOQuant

ISOQuant - Integrated SOlution for LC-MS based label-free protein QUANTification
http://www.isoquant.org
Other
0 stars 0 forks source link

Windows 10? #1

Open hwhitwell opened 4 years ago

hwhitwell commented 4 years ago

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

MatteoLacki commented 4 years ago

Dear Harry,

I will answer quickly (I don't think Jorg has to do that, he works somewhere else now). Right now we use the attached build of IsoQuant. ISOQuant.jar https://drive.google.com/file/d/1-FFaX3edJKhkBxgWay-IISrRnltvyaav/view?usp=drive_web Please install a 64bit java to run it. We do it with the following batch script: java -Xms256m -Xmx8096m -jar C:\ISOQuant\ISOQuant.jar & exit

Since you are running it on a computer with smaller RAM, I would change the -Xmx setting to 4048. Also, do not the path to the .jar file.

Before running the IsoQuant itself, SQL, you must start the Apache server and MySQL. There are preconfigured versions of these software that can be found under XAMPP (for Windows I assume) here http://www.immunologie.uni-mainz.de/isoquant/index.php?slab=download-links#download-links . I don't know if it will run on some newer versions of MySQL. I expect it to do so, but was too lazy to check it myself and figure out what settings were modified to make SQL queries faster.

We run them once on computer start-up with "C:\Program Files (x86)\XAMPP\apache_start.bat" & "C:\Program Files (x86)\XAMPP\mysql_start.bat" & exit

Best to put it as a batch script into shell:startup folder.

If you have any more questions, don't hesitate to contact us.

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 11:13 AM hwhitwell notifications@github.com wrote:

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6H2AB2FQRJPF3N2BRXL5LR4VL4VANCNFSM4PDLKVKQ .

hwhitwell commented 4 years ago

Dear Matteo,

Thank you for your quick and detailed reply. The version you have sent me has installed and opened up!

Best wishes, Harry

On Tue, Jul 21, 2020 at 10:51 AM Matteo notifications@github.com wrote:

Dear Harry,

I will answer quickly (I don't think Jorg has to do that, he works somewhere else now). Right now we use the attached build of IsoQuant. ISOQuant.jar < https://drive.google.com/file/d/1-FFaX3edJKhkBxgWay-IISrRnltvyaav/view?usp=drive_web

Please install a 64bit java to run it. We do it with the following batch script: java -Xms256m -Xmx8096m -jar C:\ISOQuant\ISOQuant.jar & exit

Since you are running it on a computer with smaller RAM, I would change the -Xmx setting to 4048. Also, do not the path to the .jar file.

Before running the IsoQuant itself, SQL, you must start the Apache server and MySQL. There are preconfigured versions of these software that can be found under XAMPP (for Windows I assume) here < http://www.immunologie.uni-mainz.de/isoquant/index.php?slab=download-links#download-links

. I don't know if it will run on some newer versions of MySQL. I expect it to do so, but was too lazy to check it myself and figure out what settings were modified to make SQL queries faster.

We run them once on computer start-up with "C:\Program Files (x86)\XAMPP\apache_start.bat" & "C:\Program Files (x86)\XAMPP\mysql_start.bat" & exit

Best to put it as a batch script into shell:startup folder.

If you have any more questions, don't hesitate to contact us.

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 11:13 AM hwhitwell notifications@github.com wrote:

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AA6H2AB2FQRJPF3N2BRXL5LR4VL4VANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661756774, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6LVCA7UIHU7YXIDGS6QX3R4VQIRANCNFSM4PDLKVKQ .

MatteoLacki commented 4 years ago

Glad to hear that.

Cheers,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 12:22 PM hwhitwell notifications@github.com wrote:

Dear Matteo,

Thank you for your quick and detailed reply. The version you have sent me has installed and opened up!

Best wishes, Harry

On Tue, Jul 21, 2020 at 10:51 AM Matteo notifications@github.com wrote:

Dear Harry,

I will answer quickly (I don't think Jorg has to do that, he works somewhere else now). Right now we use the attached build of IsoQuant. ISOQuant.jar <

https://drive.google.com/file/d/1-FFaX3edJKhkBxgWay-IISrRnltvyaav/view?usp=drive_web

Please install a 64bit java to run it. We do it with the following batch script: java -Xms256m -Xmx8096m -jar C:\ISOQuant\ISOQuant.jar & exit

Since you are running it on a computer with smaller RAM, I would change the -Xmx setting to 4048. Also, do not the path to the .jar file.

Before running the IsoQuant itself, SQL, you must start the Apache server and MySQL. There are preconfigured versions of these software that can be found under XAMPP (for Windows I assume) here <

http://www.immunologie.uni-mainz.de/isoquant/index.php?slab=download-links#download-links

. I don't know if it will run on some newer versions of MySQL. I expect it to do so, but was too lazy to check it myself and figure out what settings were modified to make SQL queries faster.

We run them once on computer start-up with "C:\Program Files (x86)\XAMPP\apache_start.bat" & "C:\Program Files (x86)\XAMPP\mysql_start.bat" & exit

Best to put it as a batch script into shell:startup folder.

If you have any more questions, don't hesitate to contact us.

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 11:13 AM hwhitwell notifications@github.com wrote:

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AA6H2AB2FQRJPF3N2BRXL5LR4VL4VANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661756774, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AD6LVCA7UIHU7YXIDGS6QX3R4VQIRANCNFSM4PDLKVKQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661771820, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6H2AD3AZFNMCGVKOVRK6TR4VT7FANCNFSM4PDLKVKQ .

hwhitwell commented 4 years ago

Hi again,

Thank you for your support - I have another question!

I have downloaded a raw file and the PLGS files from Pride that are described in this paper:

  1. Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S Proteomics. [Online] Wiley-VCH Verlag; 2015;15(18): 3140–3151. Available from: doi:10.1002/pmic.201400396

(these are S130423_015.rar and S130423_015.raw.zip from https://www.ebi.ac.uk/pride/archive/projects/PXD001240)

However, I cannot get ISOQuant to recognise this as a PLGS project. I don't actually have PLGS at the moment, is there a way to get around this?

Thank you very much, Harry

On Tue, Jul 21, 2020 at 11:24 AM Matteo notifications@github.com wrote:

Glad to hear that.

Cheers,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 12:22 PM hwhitwell notifications@github.com wrote:

Dear Matteo,

Thank you for your quick and detailed reply. The version you have sent me has installed and opened up!

Best wishes, Harry

On Tue, Jul 21, 2020 at 10:51 AM Matteo notifications@github.com wrote:

Dear Harry,

I will answer quickly (I don't think Jorg has to do that, he works somewhere else now). Right now we use the attached build of IsoQuant. ISOQuant.jar <

https://drive.google.com/file/d/1-FFaX3edJKhkBxgWay-IISrRnltvyaav/view?usp=drive_web

Please install a 64bit java to run it. We do it with the following batch script: java -Xms256m -Xmx8096m -jar C:\ISOQuant\ISOQuant.jar & exit

Since you are running it on a computer with smaller RAM, I would change the -Xmx setting to 4048. Also, do not the path to the .jar file.

Before running the IsoQuant itself, SQL, you must start the Apache server and MySQL. There are preconfigured versions of these software that can be found under XAMPP (for Windows I assume) here <

http://www.immunologie.uni-mainz.de/isoquant/index.php?slab=download-links#download-links

. I don't know if it will run on some newer versions of MySQL. I expect it to do so, but was too lazy to check it myself and figure out what settings were modified to make SQL queries faster.

We run them once on computer start-up with "C:\Program Files (x86)\XAMPP\apache_start.bat" & "C:\Program Files (x86)\XAMPP\mysql_start.bat" & exit

Best to put it as a batch script into shell:startup folder.

If you have any more questions, don't hesitate to contact us.

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 11:13 AM hwhitwell notifications@github.com wrote:

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AA6H2AB2FQRJPF3N2BRXL5LR4VL4VANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661756774 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AD6LVCA7UIHU7YXIDGS6QX3R4VQIRANCNFSM4PDLKVKQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661771820, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AA6H2AD3AZFNMCGVKOVRK6TR4VT7FANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661772537, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6LVCEG77WFHPIHTQ6TQ23R4VUFNANCNFSM4PDLKVKQ .

MatteoLacki commented 4 years ago

Hi,

Each .raw.rar file has a corresponding .rar with search results. For instance, in file S130423_21.rar you will find xml files like S130423_21_Apex3D.xml, S130423_21_Pep3D_Spectrum.xml, and S130423_21_IA_workflow.xml. These are the results of running PLGS (or an equivalent combo of running Apex3D on the raw folder, followed by Peptide3D, followed by iaDBs). I don't know if IsoQuant can directly import those files. What we do in our lab, is the following: make a folder called S130423_21 and put the 3 xml's there. Similarly construct all the other folders for which you want to run IsoQuant's match between run algorithm. Write an excel file like the one attached. Briefly: each row contains simply absolute paths to each of the xml's: acquired_name peptide3d_xml iaDBs_xml sample_description O200326_47 Y:\RES\2018-023\O200326_47\O200326_47_Pep3D_Spectrum.xml Y:\RES\2018-023\O200326_47\O200326_47_IA_workflow.xml 2018-023-08 Alberg O200326_48 Y:\RES\2018-023\O200326_48\O200326_48_Pep3D_Spectrum.xml Y:\RES\2018-023\O200326_48\O200326_48_IA_workflow.xml 2018-023-09 Alberg

For us it is convenient, because our pipeline makes additional files that are easily collectable into such file. Unfortunately, you will have to compile them yourself.

Then: Import it from IsoQuant with IMPORT CSV, define groups, set parameters, run Full Analysis, export the peptide and protein report.

That's how it's being done now :)

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 2:43 PM hwhitwell notifications@github.com wrote:

Hi again,

Thank you for your support - I have another question!

I have downloaded a raw file and the PLGS files from Pride that are described in this paper:

  1. Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S Proteomics. [Online] Wiley-VCH Verlag; 2015;15(18): 3140–3151. Available from: doi:10.1002/pmic.201400396

(these are S130423_015.rar and S130423_015.raw.zip from https://www.ebi.ac.uk/pride/archive/projects/PXD001240)

However, I cannot get ISOQuant to recognise this as a PLGS project. I don't actually have PLGS at the moment, is there a way to get around this?

Thank you very much, Harry

On Tue, Jul 21, 2020 at 11:24 AM Matteo notifications@github.com wrote:

Glad to hear that.

Cheers,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 12:22 PM hwhitwell notifications@github.com wrote:

Dear Matteo,

Thank you for your quick and detailed reply. The version you have sent me has installed and opened up!

Best wishes, Harry

On Tue, Jul 21, 2020 at 10:51 AM Matteo notifications@github.com wrote:

Dear Harry,

I will answer quickly (I don't think Jorg has to do that, he works somewhere else now). Right now we use the attached build of IsoQuant. ISOQuant.jar <

https://drive.google.com/file/d/1-FFaX3edJKhkBxgWay-IISrRnltvyaav/view?usp=drive_web

Please install a 64bit java to run it. We do it with the following batch script: java -Xms256m -Xmx8096m -jar C:\ISOQuant\ISOQuant.jar & exit

Since you are running it on a computer with smaller RAM, I would change the -Xmx setting to 4048. Also, do not the path to the .jar file.

Before running the IsoQuant itself, SQL, you must start the Apache server and MySQL. There are preconfigured versions of these software that can be found under XAMPP (for Windows I assume) here <

http://www.immunologie.uni-mainz.de/isoquant/index.php?slab=download-links#download-links

. I don't know if it will run on some newer versions of MySQL. I expect it to do so, but was too lazy to check it myself and figure out what settings were modified to make SQL queries faster.

We run them once on computer start-up with "C:\Program Files (x86)\XAMPP\apache_start.bat" & "C:\Program Files (x86)\XAMPP\mysql_start.bat" & exit

Best to put it as a batch script into shell:startup folder.

If you have any more questions, don't hesitate to contact us.

Best wishes,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Tue, Jul 21, 2020 at 11:13 AM hwhitwell <notifications@github.com

wrote:

Dear Dr Kuharev,

I hope you are well. Having read your 201% article in Proteomics and 2016 in Nature, I would like to have a look at IsoQuant. However, I cannot get the software to run on my PC – I wandered if you may be able to offer some support.

I am running Windows 10 (10.0.17134) with 8Gb RAM and java 1.8.0 installed. I have followed the instructions on your IsoQuant webpage for installation, installing both the XAMPP for Windows (which runs) and ISOQuant for Windows. When I try and load the Isoquant exeutionable, the logo pops up, but then instantly closes. I have tried both the Windows install, and the portable versions.

Have you any suggestions? I look forward to hearing back from you,

Thanks very much!

Best wishes, Harry

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AA6H2AB2FQRJPF3N2BRXL5LR4VL4VANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661756774 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AD6LVCA7UIHU7YXIDGS6QX3R4VQIRANCNFSM4PDLKVKQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661771820 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AA6H2AD3AZFNMCGVKOVRK6TR4VT7FANCNFSM4PDLKVKQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661772537, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AD6LVCEG77WFHPIHTQ6TQ23R4VUFNANCNFSM4PDLKVKQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jkuharev/ISOQuant/issues/1#issuecomment-661834918, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6H2AC5X3ZDOBMUSTQ6UILR4WEQPANCNFSM4PDLKVKQ .

hwhitwell commented 4 years ago

Thank you for your very quick and helpful reply.

Did you mean to attached a file - I couldn't not see one. Maybe it would be easiesr to directly email me it (h.whitwell@imperial.ac.uk).

Thank you very much! Harry

jkuharev commented 4 years ago

Matteo, thank you for helping in this situation. There are many things I would do in ISOQuant somewhat differently from todays perspective. As Matteo mentioned, I don't have time to support that application. You can download the last build also directly from github: https://github.com/jkuharev/ISOQuant/tree/master/binary_distribution It should run with any recent MariaDB or MySQL build. There were some tweaks which could help with performance:

max_heap_table_size = 2048M  
tmp_table_size = 2048M  
thread_stack = 256K

see section 2 in help file: https://github.com/jkuharev/ISOQuant/blob/master/doc/help/help.pdf

Reading reorganized PLGS data from a flat folder with paths in a CSV file is an undocumented feature built over night as one of the very last things I did at the proteomics group to make the software usable in context of a computing pipeline. I do not remember details and will also not have the time to improve or even to document that.

best regards Jörg

hwhitwell commented 4 years ago

Dear Jörg,

Thanks very much for the comments and advice, Matteo has also been extremely helpful.

Best wishes Harry

Dr Harry Whitwell www.harrywhitwell.com

On 22 Jul 2020, at 06:39, Jørg Kuharev notifications@github.com wrote:

 Matteo, thank you for helping in this situation. There are many things I would do in ISOQuant somewhat differently from todays perspective. As Matteo mentioned, I don't have time to support that application. You can download the last build also directly from github: https://github.com/jkuharev/ISOQuant/tree/master/binary_distribution It should run with any recent MariaDB or MySQL build. There were some tweaks which could help with performance:

max_heap_table_size = 2048M
tmp_table_size = 2048M
thread_stack = 256K see section 2 in help file: https://github.com/jkuharev/ISOQuant/blob/master/doc/help/help.pdf

Reading reorganized PLGS data from a flat folder with paths in a CSV file is an undocumented feature built over night as one of the very last things I did at the proteomics group to make the software usable in context of a computing pipeline. I do not remember details and will also not have the time to improve or even to document that.

best regards Jörg

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.