packages-conda.yaml

---
channels:
  - bioconda
  - r
  - conda-forge
minimal:
  - awscli
  - p7zip
  - s3gof3r
bio_nextgen:
  - age-metasv
  - bamtools
  - bamutil
  - bcbio-prioritize
  - bcbio-rnaseq
  - bcbio-variation
  - bcbio-variation-recall
  - bcbreport
  - bcftools=1.3.0
  - bedtools=2.24.0
  - biobambam
  - bowtie
  - bowtie2
  - bwa
  - bwakit
  - bio-vcf
  - cage
  - cancerit-allelecount
  - cnvkit
  - cpat
  - cramtools
  - crossmap
  - cufflinks
  - cutadapt
  - delly
  - express
  - fastqc
  - freebayes=1.0.2.29
  - gatk
  - gatk-framework=3.5.21
  - geneimpacts
  - gemini
  - glpk=4.57
  - grabix
  - gsort
  - svtools
  - gvcf-regions
  - hap.py
  - hmmlearn
  - hisat2
  - htslib
  - htseq
  - impute2
  - kraken
  - lofreq
  - lumpy-sv
  - macs2
  - manta
  - mbuffer
  - metasv
  - mirdeep2
  - moreutils
  - multiqc
  - multiqc-bcbio
  - novoalign
  - oncofuse
  - optitype
  - pandoc
  - parallel
  - pbgzip
  - perl-sanger-cgp-battenberg
  - phylowgs
  - picard
  - pindel
  - platypus-variant
  - pyloh
  - pytabix
  - pythonpy
  - qsignature
  - qualimap
  - rapmap
  - razers3
  - rtg-tools
  - sailfish
  - salmon
  - sambamba
  - samblaster
  - samtools
  - simple_sv_annotation
  - scalpel
  - seqbuster
  - seqtk
  - sickle-trim
  - spades
  - snap-aligner=1.0dev.97
  - snpeff=4.2
  - star
  - stringtie
  - subread
  - svtyper
  - theta2
  - tophat
  - tdrmapper
  - ucsc-bedtobigbed
  - ucsc-bigbedinfo
  - ucsc-bigbedsummary
  - ucsc-bigbedtobed
  - ucsc-bedgraphtobigwig
  - ucsc-bigwiginfo
  - ucsc-bigwigsummary
  - ucsc-bigwigtobedgraph
  - ucsc-bigwigtowig
  - ucsc-fatotwobit
  - ucsc-gtftogenepred
  - ucsc-liftover
  - ucsc-wigtobigwig
  - wham
  - vardict
  - vardict-java
  - variantbam
  - variant-effect-predictor
  - varscan
  - vawk
  - vcfanno
  - vcf2db
  - vcflib
  - viennarna
  - vt
perl:
  - perl-app-cpanminus
  - perl-archive-extract
  - perl-archive-zip
  - perl-bio-db-sam
  - perl-cgi
  - perl-dbi
  - perl-encode-locale
  - perl-file-fetch
  - perl-file-sharedir
  - perl-file-sharedir-install
  - perl-ipc-system-simple
  - perl-lwp-simple
  - perl-lwp-protocol-https
  - perl-statistics-descriptive
  - perl-time-hires
  - perl-vcftools-vcf
r:
  - r
  - r-cghflasso
  - r-chbutils
  - r-devtools
  - r-dplyr
  - r-dt
  - r-knitr
  - r-ggdendro
  - r-ggplot2
  - r-gplots
  - r-gsalib
  - r-pheatmap
  - r-plyr
  - r-pscbs
  - r-reshape
  - r-rmarkdown
  - r-rsqlite
  - r-sleuth
  - r-snow
  - r-stringi
  - r-wasabi
  - bioconductor-annotate
  - bioconductor-biocinstaller
  - bioconductor-biocstyle
  - bioconductor-biostrings
  - bioconductor-biovizbase
  - bioconductor-bubbletree
  - bioconductor-cn.mops
  - bioconductor-degreport
  - bioconductor-deseq2
  - bioconductor-dexseq
  - bioconductor-dnacopy
  - bioconductor-genomicranges
  - bioconductor-iranges
  - bioconductor-limma
  - bioconductor-rtracklayer