IGV Automation Commands #257
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I was going through the "Using the Integrative Genomics Viewers" section of the Biostar handbook and I got to the section on automating IGV. I created the FASTA and gff file and using the app and loading from inside the app works but it will not work from the command line. It loads the sequence but nothing else.
Any ideas would be appreciated. I am frustrated by this. Thanks. |
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Replies: 1 comment 1 reply
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I suspect that the problem is that IGV runs in Windows, and the commands run from the Linux subsystem the solution would be to pass the same path to the file as it is from Windows. In Explorer, navigate to the file in question hold Shift, right-click, and select "Copy as path". That would be the name that you need to put as path to the file. https://www.howtogeek.com/670447/how-to-copy-the-full-path-of-a-file-on-windows-10/ |
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That fixed it! Thank you! |
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I suspect that the problem is that IGV runs in Windows, and the commands run from the Linux subsystem
the solution would be to pass the same path to the file as it is from Windows.
In Explorer, navigate to the file in question hold Shift, right-click, and select "Copy as path". That would be the name that you need to put as path to the file.
https://www.howtogeek.com/670447/how-to-copy-the-full-path-of-a-file-on-windows-10/