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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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Compiling jvarkit #12

Closed nmb85 closed 10 years ago

nmb85 commented 10 years ago

Hi, htsjdk compiled fine for me on my Fedora 20 system. When I try to compile jvarkit, though, I get this:

BUILD FAILED /usr/local/genome/jvarkit/build.xml:8: java.util.InvalidPropertiesFormatException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.

Followed by a string of errors. On stack exchange, this error looks like there might be something called a BOM that is messing up compilation. I don't know anything about java, though. Can you suggest what I can do to fix this? I really need that sam4weblogo tool! It's the only thing out there that will convert my sam file to a fasta alignment format!

Thanks.

lindenb commented 10 years ago

The problem is a duplicate of https://github.com/lindenb/jvarkit/issues/11 , I'm closing it.