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rekado avatar rekado commented on June 30, 2024

A workaround is to remove the "compile-htsjdk" dependency from the compile task, and to symlink the htsjdk libraries to "htsjdk/lib", which has the effect of pacifying Ant, but it would be nicer if there was a less hackish way to accomplish this.

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nh13 avatar nh13 commented on June 30, 2024

@vdauwera anyone taking a look at this? I can't un-assign myself :/

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vdauwera avatar vdauwera commented on June 30, 2024

@lbergelson any opinions about this?

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lbergelson avatar lbergelson commented on June 30, 2024

I just saw that I was tagged in this several months ago... If anyone is still interested now that we've gone to gradle... Htsjdk is no longer built as part of picard, it's pulled in from maven central. If you are running in an offline mode, you can install htsjdk into the local maven repository and picard will look for it there first.

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