environment.yml

# You can use t1is file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: rnaseq-4.1.0
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.7.10=hffdb5ce_100_cpython
  - conda-forge::pip=22.1.2=pyhd8ed1ab_0
  - conda-forge::pymdown-extensions=7.1
  - conda-forge::numpy=1.21.6=py37h976b520_0
  - conda-forge::numba=0.53.1=py37hb11d6e1_1
  - h5py=3.6.0=py37ha0f2276_0
  - conda-forge::pytest=7.1.2=py37h89c1867_0
  - bioconda::sra-tools=2.11.0=pl5321ha49a11a_3

  - bioconda::fastqc=0.11.9=hdfd78af_1
  - bioconda::trim-galore=0.6.7=hdfd78af_0
  - bioconda::multiqc=1.11=pyhdfd78af_0
  - bioconda::samtools=1.12=h9aed4be_1
  - bioconda::bcftools=1.12=h45bccc9_1
  - bioconda::star=2.7.6a=0
  - bioconda::hisat2=2.2.1=h1b792b2_3
  - bioconda::bowtie2=2.4.2=py37h8270d21_1
  - bioconda::bowtie=1.3.0=py37h9a982cc_1
  - bioconda::picard=2.25.3=hdfd78af_0
  - bioconda::preseq=3.1.2=h06ef8b0_1
  - bioconda::rseqc=4.0.0=py37h73a75cf_1
  - conda-forge::bc=1.07.1=h7f98852_0
  - bioconda::subread=2.0.1=h5bf99c6_1
  - bioconda::htseq=0.13.5=py37h9c5868f_1
  - bioconda::deeptools=3.5.1=py_0
  - bioconda::salmon=1.4.0=h84f40af_1
  - conda-forge::tbb=2020.2=hc9558a2_0
  - bioconda::qualimap=2.2.2d=1
  - bioconda::scallop=0.10.5=hbce0939_1
  - bioconda::stringtie=2.1.7=h978d192_0
  - bioconda::gffcompare=0.11.2=h7d875b9_2
  - bioconda::snpsift=4.3.1t=hdfd78af_3

  - conda-forge::r-base=4.0.3=h349a78a_8
  - conda-forge::icu=68.1=h58526e2_0
  - conda-forge::r-dplyr=1.0.9=r40h7525677_0
  - conda-forge::r-data.table=1.14.0=r40hcfec24a_0
  - conda-forge::r-gplots=3.1.1=r40hc72bb7e_0
  - conda-forge::r-matrix=1.3_2=r40he454529_0
  - conda-forge::r-proxy=0.4_25=r40hcfec24a_0
  - conda-forge::r-dendextend=1.15.1=r40hc72bb7e_0
  - conda-forge::r-pheatmap=1.0.12=r40h6115d3f_2
  - conda-forge::r-rcolorbrewer=1.1_2=r40h6115d3f_1003
  - bioconda::bioconductor-genomicfeatures=1.42.2=r40hdfd78af_0
  - bioconda::bioconductor-dupradar=1.20.0=r40hdfd78af_1
  - bioconda::bioconductor-rtracklayer=1.50.0=r40h7f5ccec_2
  - bioconda::bioconductor-genomicfeatures=1.42.2=r40hdfd78af_0
  - bioconda::bioconductor-edger=3.32.1=r40h399db7b_0
  - bioconda::bioconductor-deseq2=1.30.1=r40h399db7b_0
  - bioconda::bioconductor-tximport=1.18.0=r40hdfd78af_1

  - pip:
    - xengsort-cubic==1.1.0