Comments (4)
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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@vdauwera anyone taking a look at this? I can't un-assign myself :/
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@lbergelson any opinions about this?
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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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Related Issues (20)
- StringIndexOutOfBoundsException at LiftoverVcf HOT 3
- Error: A JNI error has occurred, please check your installation and try again HOT 1
- MarkDuplicates: Instead of adding the read group of a read to the key, picard always adds "RG"
- java.lang.NegativeArraySizeException HOT 2
- genotypeConcordance irregular behavior in counting after applying filters HOT 3
- MarkDuplicates with single end data does not write the full report HOT 3
- Picard Build Failure HOT 6
- java environment not detected when using option OUTPUT in BuilBamIndex HOT 1
- Getting Segfault when running ReorderSam via GATK HOT 1
- How to control the number of threads HOT 1
- Edge case in LiftoverVcf causes cryptic string exception HOT 8
- TAGGING_POLICY=OpticalOnly tags everything HOT 4
- Issue Running Picard MarkDuplicates: File Compression Error with Snappy HOT 1
- about MarkDuplicates HOT 1
- UnMarkDuplicate HOT 1
- Running picard in parallel issue HOT 3
- `--USE_END_IN_UNPAIRED_READS` and `--USE_UNPAIRED_CLIPPED_END` options for `picard MarkDuplicates` have no effect HOT 9
- MarkDuplicates SAM validation error HOT 6
- Optical duplicates HOT 4
- VaridateSamFile wrong NM tag computation HOT 3
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