Comments (3)
There's not only mysql. it looks like you're missing all the libraries required (htsjdk... ). Check your paths, did you install htsjdk ? did you compile after editing build.properties ?
- can you try this (of course, replace the paths with your context )
$ cd jvarkit
$ ant backlocate
$ cd dist
$ echo "#" | java -cp /home/lindenb/package/mysql-connector-java-5.1.12/mysql-connector-java-5.1.12-bin.jar::/home/lindenb/src/jvarkit-git/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/htsjdk-1.117.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/snappy-java-1.0.3-rc3.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/commons-jexl-2.1.1.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/commons-logging-1.1.1.jar:backlocate.jar com.github.lindenb.jvarkit.tools.backlocate.BackLocate
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Ah, I compliled before editing build.properties. I'll also check on building htsjdk.
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I compiled again and it works. Thank you so much, @lindenb !
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Related Issues (20)
- vcf2tab HOT 2
- Randomized runs of Biostar154220.html HOT 1
- Test AssertionError HOT 2
- build failed and test failed
- Task :vcffilterjdk FAILED HOT 1
- ./gradlew mapuniprot install error HOT 3
- Is it possible to add the 'Gene' and peptide 'POSITION(S)' info corresponding to each genomic coordinate using MapUniProtFeatures HOT 5
- Task 'MapUniProtFeatures.main()' not found in root project 'jvarkit'. HOT 2
- indel calls with msa2vcf? HOT 2
- build failed,are these packages core packages or important packages and will they affect other toolkits? HOT 2
- java.lang.StackOverflowError [Biostar175929] HOT 2
- vcf2svg
- bamrenamechr [SEVERE][ConvertBamChromosomes]Illegal state mapper==null or dict-out=null HOT 5
- questions about sam2tsv output file HOT 4
- Backlocate w/ E. coli genome HOT 3
- Biostar404363 – unequal AF instead of ambiguity code HOT 6
- Biostar139647 : documentation issues HOT 2
- jvarkit as conda package HOT 11
- Task 'sortsamrefname' not found in root project 'jvarkit'. HOT 3
- Bug in msa2vcf ? HOT 4
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