The “generate-jar-indices” phase fails on a couple of packages, such as
java-picard (all variants) dropseq-tools java-cisd-jhdf5 The errors are either about duplicates as in java-picard-2.10.3: duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class or about missing files as in dropseq-tools: java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar I have removed the phase in these packages, but that’s not ideal. Can we make this phase more robust? -- Ricardo