# Packages available in the Homebrew and Linuxbrew package manager
---
minimal:
  - cmake
  - s3gof3r
perl:
  - cpanminus
bio_nextgen:
  alignment:
    - bwa
    - bowtie2 
    - novoalign
    - rna-star
    # - snap-aligner # Needs sync with homebrew-cbl/homebrew-science and compile on older gcc
    - tophat-binary
  utilities:
    - bamtools
    - bedtools
    - cramtools
    - biobambam
    - express-binary
    - fastqc
    - grabix
    - picard-tools
    - qualimap
    - kraken
    - sambamba-binary
    - samblaster
    - seqtk
    - speedseq
    - staden_io_lib
    - oncofuse
    - sickle
  analysis:
    - cufflinks-binary
    - samtools;--without-curses
    - htslib
    - bcftools
  variant:
    - bcbio-variation-recall
    - delly;--with-binary
    - freebayes
    - gatk-framework
    #- glia  # Needs updates to fsom
    - hall-lab-sv-tools
    - lofreq
    - lumpy-sv
    - pindel
    - platypus-variant
    - rtg-tools
    - scalpel
    - snpeff
    - theta2
    - vardict
    - vardict-java
    - vcflib
    - vep
    - wham;--with-binary
    - qsignature
    - qsnp
    # - vcftools # Build problems with default libz on Ubuntu 12.04
    - vt;--with-binary

# Packages available in the Homebrew and Linuxbrew package manager
---
minimal:
  - cmake
  - s3gof3r
perl:
  - cpanminus
bio_nextgen:
  alignment:
    - bwa
    - bwakit
    - bowtie2 
    - novoalign
    - rna-star
    # - snap-aligner # Needs sync with homebrew-cbl/homebrew-science and compile on older gcc
    - tophat-binary
  utilities:
    - bamtools
    - bedtools
    - cramtools
    - biobambam
    - express-binary
    - fastqc
    - grabix
    - picard-tools
    - qualimap
    - kraken
    - sambamba-binary
    - samblaster
    - seqtk
    - speedseq
    - staden_io_lib
    - oncofuse
    - sickle
  analysis:
    - cufflinks-binary
    - samtools;--without-curses
    - htslib
    - bcftools
  variant:
    - bcbio-variation-recall
    - delly;--with-binary
    - freebayes
    - gatk-framework
    #- glia  # Needs updates to fsom
    - hall-lab-sv-tools
    - lofreq
    - lumpy-sv
    - pindel
    - platypus-variant
    - rtg-tools
    - scalpel
    - snpeff
    - theta2
    - vardict
    - vardict-java
    - vcflib
    - vep
    - wham;--with-binary
    - qsignature
    - qsnp
    # - vcftools # Build problems with default libz on Ubuntu 12.04
    - vt;--with-binary

Include bwakit in bcbio for hg38 support
Include bwakit in bcbio for hg38 support
