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Bug 671632 - sci-biology/picard - error: no main manifest attribute, in /usr/share/picard/lib/picard.jar
Summary: sci-biology/picard - error: no main manifest attribute, in /usr/share/picard/...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
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Depends on:
Blocks:
 
Reported: 2018-11-21 12:23 UTC by Vytautas
Modified: 2021-05-04 02:42 UTC (History)
0 users

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Runtime testing required: ---

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Description Vytautas 2018-11-21 12:23:29 UTC 
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.
Comment 1 Martin Mokrejš 2020-10-18 11:02:48 UTC 
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