The conda version doesn't have the package I need.

[zhujiahua700403]

Subject of the issue

I want to use the BreakdancerToVcf package under Jvarkit, however, after downloading it I realized that this package is not in the file downloaded under conda, how should I get this package?

[lindenb]

@zhujiahua700403 Hi, it was not included in the 'big' jar because it's mostly unused and BreakDancer is pretty old, many SV caller outperform breakdancer now.

You can alway download the sources and run:

 ./gradlew breakdancer2vcf

that should create a standalone jar under the dist directory

$ java -jar dist/breakdancer2vcf.jar -h
Usage: breakdancer2vcf [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -R, -reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict