# Packages available in the Homebrew and Linuxbrew package manager
---
minimal:
  - cmake
perl:
  - cpanminus
bio_nextgen:
  alignment:
    - bwa
#    - bowtie2       (2.2.0 doesn't work with Tophat, so use the source version for now)
    - novoalign
    - rna-star
  utilities:
    - bamtools
    - bedtools
    - cramtools
    - libmaus
    - biobambam
    - fastqc
    - qualimap
    - kraken
    - sambamba
    - samblaster
    - seqtk==HEAD
    - speedseq
    - staden_io_lib
    - oncofuse
  analysis:
    #- cufflinks
    - samtools
    - htslib
    - bcftools
    #- tophat
  variant:
    - freebayes
    - gatk-framework
    - glia
    - hall-lab-sv-tools
    - lumpy-sv
    - platypus-variant
    - rtg-tools
    - scalpel
    - snpeff
    - vardict
    - vcflib
    - vep
    - qsignature
    # - vcftools # Build problems with default libz on Ubuntu 12.04
    - vt

# Packages available in the Homebrew and Linuxbrew package manager
---
minimal:
  - cmake
perl:
  - cpanminus
bio_nextgen:
  alignment:
    - bwa
#    - bowtie2       (2.2.0 doesn't work with Tophat, so use the source version for now)
    - novoalign
    - rna-star
  utilities:
    - bamtools
    - bedtools
    - cramtools
    - libmaus
    - biobambam
    - fastqc
    - qualimap
    - kraken
    - sambamba
    - samblaster
    - seqtk==HEAD
    - speedseq
    - staden_io_lib
    - oncofuse
    - sickle
  analysis:
    #- cufflinks
    - samtools
    - htslib
    - bcftools
    #- tophat
  variant:
    - freebayes
    - gatk-framework
    - glia
    - hall-lab-sv-tools
    - lumpy-sv
    - platypus-variant
    - rtg-tools
    - scalpel
    - snpeff
    - vardict
    - vcflib
    - vep
    - qsignature
    # - vcftools # Build problems with default libz on Ubuntu 12.04
    - vt

Add sickle to ngs pipeline dependencies.
Add sickle to ngs pipeline dependencies.
