environment.yml

# phage_analysis — single conda environment
# Target: Python 3.9 (best common ground across all tools)
#
# Install:
#   conda env create -f environment.yml   (or: mamba env create -f environment.yml)
#   conda activate phage_analysis
#
# Version notes:
#   - bacphlip 0.9.6: conda package hard-pins scikit-learn 0.23.1, which conflicts
#     with vContact2. Installed via pip instead — predictions still work with sklearn 1.x.
#   - virsorter (VirSorter2): bioconda package name is 'virsorter', not 'virsorter2'.
#     DB setup: run 'virsorter setup -d <db_dir> -j <threads>' after install.
#   - vHULK: not in bioconda; installed via pip. Requires TensorFlow 2.9 (py3.9 compat).
#   - vContact2: requires networkx 2.x API; pinned to networkx>=2.7,<3.0.
#   - Nextflow: Java 17 comes from this environment. Set JAVA_HOME=$CONDA_PREFIX.

name: phage_analysis

channels:
  - gultekinunal
  - conda-forge
  - bioconda
  - defaults

dependencies:
  # ── Python ───────────────────────────────────────────────────────────────────
  - python=3.9

  # ── Java + Nextflow ───────────────────────────────────────────────────────────
  - openjdk=17
  - nextflow>=23.04.0

  # ── QC & trimming ─────────────────────────────────────────────────────────────
  - fastqc=0.12.1
  - fastp>=0.23
  - multiqc>=1.21

  # ── Taxonomic classification ──────────────────────────────────────────────────
  - kraken2=2.1.3

  # ── Assembly ──────────────────────────────────────────────────────────────────
  - spades>=4.0

  # ── Viral sequence detection (package name: virsorter, not virsorter2) ────────
  - virsorter=2.2.4

  # ── Genome quality ────────────────────────────────────────────────────────────
  - checkv=1.0.1

  # ── Annotation ────────────────────────────────────────────────────────────────
  - pharokka>=1.7.3
  - prokka=1.14.6

  # ── Viral taxonomy clustering ─────────────────────────────────────────────────
  - vcontact2=0.11.3
  - clusterone=1.0
  - networkx>=2.7,<3.0

  # ── Host prediction (TensorFlow for vHULK) ────────────────────────────────────
  - tensorflow>=2.9,<2.13
  - keras>=2.9,<2.13

  # ── Shared bioinformatics tools ───────────────────────────────────────────────
  - blast=2.15.0
  - diamond>=2.1
  - hmmer>=3.4
  - prodigal>=2.6.3
  - mash>=2.3
  - aragorn>=1.2
  - trnascan-se>=2.0
  - minced>=0.4

  # ── Python libraries ──────────────────────────────────────────────────────────
  - biopython>=1.79
  - numpy>=1.21,<2.0
  - pandas>=1.3,<2.0
  - scipy>=1.7
  - matplotlib-base>=3.5
  - pyhmmer>=0.10
  - scikit-learn>=1.0,<1.2

  # ── vHULK (gultekinunal conda channel) ───────────────────────────────────────
  - vhulk=2.0.0

  # ── pip installs ──────────────────────────────────────────────────────────────
  # screed ve bacphlip Dockerfile'da ayrıca kurulur (pip metadata sorunu)
  - pip