environment.yaml

name: spacemake
channels:
    - bih-cubi
    - conda-forge
    - bioconda
    - nodefaults
dependencies:
    - python>=3.6,<3.12
    - snakemake>=5.32.0,<6.4.0
    - star>=2.7.1a
    - samtools>=1.13
    - sambamba>=0.6.8
    - bowtie2>=2.3.4
    - bcl2fastq2>=2.19
    - fastqc>=0.11.9
    - pip>=21.1
    - r-base>=4.0.3
    - r-rmarkdown>=2.7
    - r-tidyverse>=1.3.1
    - r-kableextra>=1.3.4
    - r-cowplot>=1.1.1
    - r-pals>=1.7
    - r-hexbin
    - r-scales
    - pysam>=0.16.0.1
    - pot
    - openjdk==11.0.15
    - pigz
    - pip:
        - setproctitle
        - isal
        - pytest
        - pytest-cov
        - mrfifo>=0.3.0
        - pandas>2
        - scanpy>=1.8.1
        - leidenalg>=0.8.1
        - numpy>=1.18.1
        - more-itertools>=8.7.0
        - biopython>=1.78
        - scipy>=1.5.0
        - scikit-misc>=0.1.3
        - scikit-learn>=0.23.1
        - squidpy>=1.0.0
        - novosparc
        - opencv-python
        - jinja2>=3.1.3
        - matplotlib==3.8.4
#        - pytest-optional-tests