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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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Canvas installation #115

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

Sorry I downloaded and uncompressed Canvas-1.39.0.1598+master_x64 but when I am typing 


[fi1d18@cyan01 ~]$ cd /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/
[fi1d18@cyan01 Canvas-1.39.0.1598+master_x64]$ Canvas.exe --help                      -bash: Canvas.exe: command not found
[fi1d18@cyan01 Canvas-1.39.0.1598+master_x64]$ Canvas.dll --help
-bash: ./Canvas.dll: Permission denied
[fi1d18@cyan01 Canvas-1.39.0.1598+master_x64]$
eroller commented 5 years ago

you need to dotnet runtime (similar to java runtime for a java application):

/path/to/dotnet Canvas.dll --help

Please see the README for where to download dotnet.

beginner984 commented 5 years ago

Sorry I can not figure out what to do, I have already downloaded dotnet

[fi1d18@cyan01 ~]$ /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/Canvas.dll --help
-bash: /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/Canvas.dll: Permission denied
[fi1d18@cyan01 ~]$ dotnet /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/Canvas.dll --help
-bash: dotnet: command not found
[fi1d18@cyan01 ~]$
eroller commented 5 years ago

bash cannot find dotnet. Where did you install it?

beginner984 commented 5 years ago 
[fi1d18@cyan01 fi1d18]$ /temp/hgig/fi1d18/bin/dotnet /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/Canvas.dll --help
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /temp/hgig/fi1d18/bin/dotnet)

Sorry I downloaded aspnetcore-runtime-2.2.3-linux-x64.tar.gz and extracted that to a folder, in this folder host, shared, dotnet created

I can not figure out which dotnet I should refer to :(

eroller commented 5 years ago

try using this version of dotnet:

https://dotnet.microsoft.com/download/thank-you/dotnet-runtime-2.1.9-linux-x64-binaries

What OS are you running?

beginner984 commented 5 years ago

Linux cyan01

Sorry I downloaded what you kindly suggested and extracted that in a folder named bin and I tried 


(py3venv) [fi1d18@cyan01 fi1d18]$ /temp/hgig/fi1d18/bin/dotnet /temp/hgig/fi1d18/Canvas-1.39.0.1598+master_x64/Canvas.dll --help
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.17' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.5' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by /temp/hgig/fi1d18/bin/dotnet)
/temp/hgig/fi1d18/bin/dotnet: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /temp/hgig/fi1d18/bin/dotnet)