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compbiocore / VariantVisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
https://compbiocore.github.io/VariantVisualization.jl/stable/
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difficulty installing and using VIVA #83

Closed helbacsb closed 3 years ago

helbacsb commented 4 years ago

Hy, I installed the Julia environment and VariantVisualization, but couldn't make it work. When giving the command: viva -f Pac14_cl7_1.vcf -s -o output / directory the following occurs ERROR: syntax: extra token "Pac14_cl7_1" after end of expression.

What it is? Which directory should the .vcf file be?

Thank you very much in advance, Helba Cirino.

gtollefson commented 4 years ago

Hi @helbacsb,

Thanks for posting your question. Try running 'viva -f Pac14_cl7_1.vcf -s html'.

The parameter '-s' is missing an argument in the command line code you pasted above. By default, without specifying '-s', VIVA saves html files.

Also, in the parameter: '-o output / directory', there should not be spaces in the argument. It should be '-o output/directory'. If that's the same code you ran, that should cause an error too.

The .vcf file can be in any directory. You can specify a full file path with the 'f' flag, or just the .vcf filename if you are within its directory. The output files will be saved in the directory where you are running the tool from by default, otherwise you can specify the exact output path with the '-o' parameter.

Let me know how it goes! George

gtollefson commented 4 years ago

@helbacsb , I just want to follow up with you about your issue. Have you been able to try running the code I suggested?

helbacsb commented 4 years ago

I still couldn't use the command. when I use julia> viva -f C: \ Users \ Adenina \ Documents \ Helba_Cirino \ Heart Diseases \ vcf \ Pac14_cl7_1.vcf -s html The following error appears: ERROR: syntax: extra token "C" after end of expression Stacktrace: [1] top-level scope at none: 0

Em sex., 15 de nov. de 2019 às 14:21, George Tollefson < notifications@github.com> escreveu:

@helbacsb https://github.com/helbacsb , I just want to follow up with you about your issue. Have you been able to try running the code I suggested?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO62S3RLUM5TRJL253BTQT3K7ZA5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEGDXCA#issuecomment-554449800, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO66IN663JATFADA2MEDQT3K7ZANCNFSM4JMEPGOQ .

-- Helba Cirino

gtollefson commented 4 years ago

@helbacsb It looks like there are spaces in your path to the VCF file. The path needs to be one continuous string with no spaces. This will cause the error you described.

Try running: 'viva -f C:\Users\Adenina\Documents\Helba_Cirino\Heart Diseases\vcf\Pac14_cl7_1.vcf -s html' instead.

helbacsb commented 4 years ago

There are no spaces in the file path. Image attached. I don't know if I could configure the windows 10 PATH as per the instruction:

To add Julia to the PATH on Windows 7 or Windows 10:

Add the path to the Julia binaries (C:\Program Files\Julia\bin) to the PATH following the concise instructions found here https://www.java.com/en/download/help/path.xml

Em seg., 18 de nov. de 2019 às 11:32, George Tollefson < notifications@github.com> escreveu:

@helbacsb https://github.com/helbacsb It looks like there are spaces in your path to the VCF file. The path needs to be one continuous string with no spaces. This will cause the error you described.

Try running: 'viva -f C:\Users\Adenina\Documents\Helba_Cirino\Heart Diseases\vcf\Pac14_cl7_1.vcf -s html' instead.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO62JG36LDLLB6GIA2CLQUKRRLA5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEKT3SI#issuecomment-555040201, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO64YWJGYHE65RJGYW43QUKRRLANCNFSM4JMEPGOQ .

-- Helba Cirino

gtollefson commented 4 years ago

@helbacsb I think I see the issue - you should not run the script from within the julia REPL. You run directly from the powershell by running viva [options]without calling julia since a symlink to julia viva is built during VariantVisualization.jl package installation.

helbacsb commented 4 years ago

When I run by powerShell it asks to open the viva file by some text editor ???

Em seg., 18 de nov. de 2019 às 14:56, George Tollefson < notifications@github.com> escreveu:

@helbacsb https://github.com/helbacsb I see - you should not run the script from within julia. I see you're running it from wihin the REPL. You should be able to run directly from the powershell by running 'viva [options]' without calling 'juila'

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO66FIC4YB4WSV3JCEJTQULJNDA5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEELKTVY#issuecomment-555133399, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO6YKKPGPUW2TN4H6YGTQULJNDANCNFSM4JMEPGOQ .

-- Helba Cirino

gtollefson commented 4 years ago

Ok, @helbacsb, since you said that you installed VariantVisualization.jl, the symlink should have been built or else thrown an error during installation. Do you receive warnings or errors when you run build VariantVisualization from within the Julia REPL? Also, can you tell me what Julia version and operating system you are running on?

It sounds like the symlink wasn't built successfully for some reason, but it is strange that there was no error during installation. Let's solve this!

helbacsb commented 4 years ago

When installing again just updates. apparently installed.

Em seg., 18 de nov. de 2019 às 16:40, George Tollefson < notifications@github.com> escreveu:

Ok, @helbacsb https://github.com/helbacsb, since you said that you installed VariantVisualization.jl, the symlink should have been built or else thrown an error during installation. Do you receive warnings or errors when you run build VariantVisualization from within the Julia REPL? Also, can you tell me what Julia version and operating system you are running on?

It sounds like the symlink wasn't built successfully for some reason, but it is strange that there was no error during installation. Let's solve this!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO63VEFAY536IZ2YFCLLQULVRRA5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEELVBXA#issuecomment-555176156, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO62OD5BGFNOCU4UT2RDQULVRRANCNFSM4JMEPGOQ .

-- Helba Cirino

helbacsb commented 4 years ago

Is the installation ok?

Em ter., 19 de nov. de 2019 às 12:33, Helba Cirino helbacsb@gmail.com escreveu:

When installing again just updates. apparently installed.

Em seg., 18 de nov. de 2019 às 16:40, George Tollefson < notifications@github.com> escreveu:

Ok, @helbacsb https://github.com/helbacsb, since you said that you installed VariantVisualization.jl, the symlink should have been built or else thrown an error during installation. Do you receive warnings or errors when you run build VariantVisualization from within the Julia REPL? Also, can you tell me what Julia version and operating system you are running on?

It sounds like the symlink wasn't built successfully for some reason, but it is strange that there was no error during installation. Let's solve this!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO63VEFAY536IZ2YFCLLQULVRRA5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEELVBXA#issuecomment-555176156, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO62OD5BGFNOCU4UT2RDQULVRRANCNFSM4JMEPGOQ .

-- Helba Cirino

-- Helba Cirino

gtollefson commented 4 years ago

@helbacsb Sorry for the delay. I think I've figured it out - there's another step outlined in our docs. Perhaps we can make our installation documentation more clear. Once you've installed the package and run 

viva -f C:\Users\Adenina\Documents\Helba_Cirino\Heart Diseases\vcf\Pac14_cl7_1.vcf
-s html

You are prompted to open the script with a text editor. You should also be able to select another application to open the script. Select the Julia executable, that is normally located at C:\Users\\AppData\Local\Julia-\bin. Let me know if this works!

helbacsb commented 4 years ago

I am using windows 10. Which step is missing?

Em qui., 21 de nov. de 2019 às 14:45, George Tollefson < notifications@github.com> escreveu:

@helbacsb https://github.com/helbacsb Sorry for the delay. I think I've figured it out - there's another step outlined in our docs. Perhaps we can make our installation documentation more clear. Once you've installed the package and run ``` viva -f C:\Users\Adenina\Documents\Helba_Cirino\Heart Diseases\vcf\Pac14_cl7_1.vcf -s html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compbiocore/VariantVisualization.jl/issues/83?email_source=notifications&email_token=ANYAO67J5MROLABTMUDA4NLQU3CM3A5CNFSM4JMEPGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEE3CMMI#issuecomment-557196849, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYAO6YDVAG6NGDMRKHHLWLQU3CM3ANCNFSM4JMEPGOQ .

-- Helba Cirino

gtollefson commented 4 years ago

@helbacsb When you run viva, you told me that you are prompted to open viva with a text editor. Is there an option to select another program to open the viva script? In Windows 10, this prompt should allow you to select another app.

The step that you need to do, is select another application to open the script instead of a text editor. You need to select the Julia executable, that is normally located at C:\Users\AppData\Local\Julia-\bin.

gtollefson commented 3 years ago

@helbacsb I'm going to close this issue since it's been over a year without reply. Please feel free to reopen it at anytime.