environment.yml

name: qcpipeline

channels:
   - anaconda
   - conda-forge
   - bioconda
   - r
   - kapabix

dependencies:

   # for the pipeline
   - bioconda::cutadapt=1.18
   - bioconda::fastq-screen=0.13.0
   - bioconda::bowtie2 # for fastq screen
   - bioconda::fastqc=0.11.8
     #- bioconda::htseq=0.11.0
   - bioconda::picard=2.18.21
   - bioconda::rsem=1.3.1
   - bioconda::rseqc=3.0.0
   - bioconda::samtools=1.3 # this version because of rsem
   - bioconda::seqtk=1.3
   - bioconda::star=2.6.1b
     #- conda-forge::pandas=0.24.1
   - kapabix::rnaseqc=1.1.8
   - conda-forge::libiconv=1.15 # required by an R calling with picard multime
   - r::r=3.4.1 # this version because of a conflict with rsem
     #- conda-forge::libgcc=7.2.0 # for custom cpp scripts
     #- conda-forge::libstdcxx-ng=7.3.0 # for custom cpp scripts
   - anaconda::libgcc-ng=8.2.0 # for custom cpp scripts
   - anaconda::libstdcxx-ng=8.2.0 # for custom cpp scripts

   # multiqc plugins
   - anaconda::numpy=1.15.4 # for one multiqc module of the multiqc plugin
   - bioconda::htseq=0.11.0 # for multiqc
   - bioconda::multiqc=1.6
   - conda-forge::openblas=0.3.3 # for multiqc, this version because of numpy
   - conda-forge::pandas=0.24.1 # for multiqc
   - pip:
      - git+https://github.com/crickbabs/BABS-MultiQC-QualityControl