I did: emerge sci-biology/picard And I did not found picard command after that so I tried: # java -jar /usr/share/picard/lib/picard.jar that gave error: no main manifest attribute, in /usr/share/picard/lib/picard.jar I suspect some flaw in ebuild file as manual install works.
Upstream dropped apache ant support (refer to build.xml in the source tarball) to gradle. The last release which is available is sci-biology/picard-1.103::gentoo . It installs properly now: # equery files picard * Searching for picard ... * Contents of sci-biology/picard-1.103: /usr /usr/bin /usr/bin/AddOrReplaceReadGroups /usr/bin/BamIndexStats /usr/bin/BamToBfq /usr/bin/BuildBamIndex /usr/bin/CalculateHsMetrics /usr/bin/CheckIlluminaDirectory /usr/bin/CleanSam /usr/bin/CollectAlignmentSummaryMetrics /usr/bin/CollectGcBiasMetrics /usr/bin/CollectInsertSizeMetrics /usr/bin/CollectMultipleMetrics /usr/bin/CollectRnaSeqMetrics /usr/bin/CollectTargetedPcrMetrics /usr/bin/CompareSAMs /usr/bin/CreateSequenceDictionary /usr/bin/DownsampleSam /usr/bin/EstimateLibraryComplexity /usr/bin/ExtractIlluminaBarcodes /usr/bin/ExtractSequences /usr/bin/FastqToSam /usr/bin/FilterSamReads /usr/bin/FixMateInformation /usr/bin/IlluminaBasecallsToFastq /usr/bin/IlluminaBasecallsToSam /usr/bin/IntervalListTools /usr/bin/MakeSitesOnlyVcf /usr/bin/MarkDuplicates /usr/bin/MarkIlluminaAdapters /usr/bin/MeanQualityByCycle /usr/bin/MergeBamAlignment /usr/bin/MergeSamFiles /usr/bin/MergeVcfs /usr/bin/NormalizeFasta /usr/bin/QualityScoreDistribution /usr/bin/ReorderSam /usr/bin/ReplaceSamHeader /usr/bin/RevertSam /usr/bin/SamFormatConverter /usr/bin/SamToFastq /usr/bin/SortSam /usr/bin/SplitVcfs /usr/bin/ValidateSamFile /usr/bin/VcfFormatConverter /usr/bin/ViewSam /usr/share /usr/share/picard /usr/share/picard/lib /usr/share/picard/lib/AddOrReplaceReadGroups.jar /usr/share/picard/lib/BamIndexStats.jar /usr/share/picard/lib/BamToBfq.jar /usr/share/picard/lib/BuildBamIndex.jar /usr/share/picard/lib/CalculateHsMetrics.jar /usr/share/picard/lib/CheckIlluminaDirectory.jar /usr/share/picard/lib/CleanSam.jar /usr/share/picard/lib/CollectAlignmentSummaryMetrics.jar /usr/share/picard/lib/CollectGcBiasMetrics.jar /usr/share/picard/lib/CollectInsertSizeMetrics.jar /usr/share/picard/lib/CollectMultipleMetrics.jar /usr/share/picard/lib/CollectRnaSeqMetrics.jar /usr/share/picard/lib/CollectTargetedPcrMetrics.jar /usr/share/picard/lib/CompareSAMs.jar /usr/share/picard/lib/CreateSequenceDictionary.jar /usr/share/picard/lib/DownsampleSam.jar /usr/share/picard/lib/EstimateLibraryComplexity.jar /usr/share/picard/lib/ExtractIlluminaBarcodes.jar /usr/share/picard/lib/ExtractSequences.jar /usr/share/picard/lib/FastqToSam.jar /usr/share/picard/lib/FilterSamReads.jar /usr/share/picard/lib/FixMateInformation.jar /usr/share/picard/lib/IlluminaBasecallsToFastq.jar /usr/share/picard/lib/IlluminaBasecallsToSam.jar /usr/share/picard/lib/IntervalListTools.jar /usr/share/picard/lib/MakeSitesOnlyVcf.jar /usr/share/picard/lib/MarkDuplicates.jar /usr/share/picard/lib/MarkIlluminaAdapters.jar /usr/share/picard/lib/MeanQualityByCycle.jar /usr/share/picard/lib/MergeBamAlignment.jar /usr/share/picard/lib/MergeSamFiles.jar /usr/share/picard/lib/MergeVcfs.jar /usr/share/picard/lib/NormalizeFasta.jar /usr/share/picard/lib/QualityScoreDistribution.jar /usr/share/picard/lib/ReorderSam.jar /usr/share/picard/lib/ReplaceSamHeader.jar /usr/share/picard/lib/RevertSam.jar /usr/share/picard/lib/SamFormatConverter.jar /usr/share/picard/lib/SamToFastq.jar /usr/share/picard/lib/SortSam.jar /usr/share/picard/lib/SplitVcfs.jar /usr/share/picard/lib/ValidateSamFile.jar /usr/share/picard/lib/VcfFormatConverter.jar /usr/share/picard/lib/ViewSam.jar /usr/share/picard/lib/picard.jar /usr/share/picard/lib/sam.jar /usr/share/picard/lib/tribble.jar /usr/share/picard/lib/variant.jar /usr/share/picard/package.env