Installing scAVENGERS

Installation

The required softwares and packages are provided as a conda environment. Conda (https://www.anaconda.com/products/distribution) helps users to manage multiple packages easily. Running below will clone scAVENGERS repository create an environment named ‘scavengers.’

wget https://github.com/kaistcbfg/scAVENGERS/archive/refs/tags/v0.1.0.tar.gz
tar -xvzf v0.1.0.tar.gz
conda env create -f scAVENGERS/envs/environment.yaml

Requirements

The program is successfully tested under the environment below. Some of the requirements are automatically installed when scAVENGERS pipeline is executed.

External tools

name

version

remarks

freebayes

1.3.5

strelka2

2.9.10

Automatically downloaded by the shell script when the pipeline is excuted.

vartrix

1.1.22

bcftools

1.12

souporcell

2.0

Automatically downloaded and compiled by the shell script when the pipeline is executed. Troublet program will only be used among the whole pipeline.

snakemake

7.3.8

Python and its packages

name

version

remarks

python

3.8.12

numba

0.54.1

numpy

1.20.3

pandas

1.4.0

scikit-learn

1.0.2

scipy

1.7.3

pystan

2.19.1.1

Provided in another environment used for ambient variant detection

Rust

name

version

remarks

rust

1.59.0

These dependencies are provided in a conda environment below.

name: scavengers
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - aioeasywebdav=2.4.0=py38h578d9bd_1001
  - aiohttp=3.8.1=py38h0a891b7_1
  - aiosignal=1.2.0=pyhd8ed1ab_0
  - amply=0.1.4=py_0
  - appdirs=1.4.4=pyh9f0ad1d_0
  - async-timeout=4.0.2=pyhd8ed1ab_0
  - attmap=0.13.2=pyhd8ed1ab_0
  - attrs=21.4.0=pyhd8ed1ab_0
  - backports=1.0=py_2
  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
  - bc=1.07.1=h7f98852_0
  - bcftools=1.12=h45bccc9_1
  - bcrypt=3.2.0=py38h497a2fe_2
  - binutils_impl_linux-64=2.36.1=h193b22a_2
  - boto3=1.21.38=pyhd8ed1ab_0
  - botocore=1.24.38=pyhd8ed1ab_0
  - brotlipy=0.7.0=py38h0a891b7_1004
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.18.1=h7f98852_0
  - ca-certificates=2022.6.15=ha878542_0
  - cachetools=5.0.0=pyhd8ed1ab_0
  - certifi=2022.6.15=py38h578d9bd_0
  - cffi=1.15.0=py38h3931269_0
  - charset-normalizer=2.0.12=pyhd8ed1ab_0
  - coin-or-cbc=2.10.7=h3786ebc_0
  - coin-or-cgl=0.60.3=he7e83c3_2
  - coin-or-clp=1.17.6=h256e9bb_3
  - coin-or-osi=0.108.6=h3b589db_2
  - coin-or-utils=2.11.6=h573740c_0
  - coincbc=2.10.7=0_metapackage
  - colorama=0.4.4=pyh9f0ad1d_0
  - conda=4.13.0=py38h578d9bd_1
  - conda-package-handling=1.8.1=py38h0a891b7_1
  - configargparse=1.5.3=pyhd8ed1ab_0
  - connection_pool=0.0.3=pyhd3deb0d_0
  - cryptography=36.0.2=py38h2b5fc30_1
  - datrie=0.8.2=py38h497a2fe_3
  - decorator=5.1.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - docutils=0.18.1=py38h578d9bd_1
  - dropbox=11.29.0=pyhd8ed1ab_0
  - filechunkio=1.8=py_2
  - filelock=3.6.0=pyhd8ed1ab_0
  - freebayes=1.3.5=py38ha193a2f_3
  - frozenlist=1.3.0=py38h0a891b7_1
  - ftputil=5.0.3=pyhd8ed1ab_0
  - gcc_impl_linux-64=11.2.0=h82a94d6_15
  - gitdb=4.0.9=pyhd8ed1ab_0
  - gitpython=3.1.27=pyhd8ed1ab_0
  - google-api-core=2.5.0=pyhd8ed1ab_0
  - google-api-python-client=2.43.0=pyhd8ed1ab_0
  - google-auth=2.6.3=pyh6c4a22f_0
  - google-auth-httplib2=0.1.0=pyhd8ed1ab_0
  - google-cloud-core=2.2.2=pyh6c4a22f_0
  - google-cloud-storage=2.1.0=pyh6c4a22f_0
  - google-crc32c=1.1.2=py38h8838a9a_2
  - google-resumable-media=2.1.0=pyh6c4a22f_0
  - googleapis-common-protos=1.56.0=py38h578d9bd_0
  - grpcio=1.45.0=py38ha0cdfde_0
  - gsl=2.6=he838d99_2
  - htslib=1.12=h9093b5e_1
  - httplib2=0.20.4=pyhd8ed1ab_0
  - icu=70.1=h27087fc_0
  - idna=3.3=pyhd8ed1ab_0
  - importlib-metadata=4.11.3=py38h578d9bd_1
  - importlib_resources=5.6.0=pyhd8ed1ab_1
  - iniconfig=1.1.1=pyh9f0ad1d_0
  - jinja2=3.1.1=pyhd8ed1ab_0
  - jmespath=1.0.0=pyhd8ed1ab_0
  - joblib=1.1.0=pyhd8ed1ab_0
  - jsonschema=4.4.0=pyhd8ed1ab_0
  - jupyter_core=4.9.2=py38h578d9bd_0
  - kernel-headers_linux-64=2.6.32=he073ed8_15
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.19.3=h3790be6_0
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - libarchive=3.5.2=hb890918_2
  - libblas=3.9.0=12_linux64_openblas
  - libcblas=3.9.0=12_linux64_openblas
  - libcrc32c=1.1.2=h9c3ff4c_0
  - libcurl=7.83.1=h7bff187_0
  - libdeflate=1.7=h7f98852_5
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-devel_linux-64=11.2.0=h0952999_15
  - libgcc-ng=12.1.0=h8d9b700_16
  - libgfortran-ng=11.2.0=h69a702a_11
  - libgfortran5=11.2.0=h5c6108e_11
  - libgomp=12.1.0=h8d9b700_16
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=12_linux64_openblas
  - liblapacke=3.9.0=12_linux64_openblas
  - libllvm11=11.1.0=hf817b99_2
  - libmamba=0.24.0=hd8a31e3_1
  - libmambapy=0.24.0=py38h923e62a_1
  - libnghttp2=1.47.0=h727a467_0
  - libnsl=2.0.0=h7f98852_0
  - libopenblas=0.3.18=pthreads_h8fe5266_0
  - libprotobuf=3.20.0=h6239696_0
  - libsanitizer=11.2.0=he4da1e4_15
  - libsodium=1.0.18=h36c2ea0_1
  - libsolv=0.7.22=h6239696_0
  - libssh2=1.10.0=ha56f1ee_2
  - libstdcxx-ng=12.1.0=ha89aaad_16
  - libxml2=2.9.14=h22db469_0
  - libzlib=1.2.11=h36c2ea0_1013
  - llvmlite=0.37.0=py38h4630a5e_1
  - logmuse=0.2.6=pyh8c360ce_0
  - lz4-c=1.9.3=h9c3ff4c_1
  - lzo=2.10=h516909a_1000
  - mamba=0.24.0=py38h1abaa86_1
  - markupsafe=2.1.1=py38h0a891b7_1
  - multidict=6.0.2=py38h0a891b7_1
  - nbformat=5.3.0=pyhd8ed1ab_0
  - ncurses=6.2=h58526e2_4
  - nomkl=1.0=h5ca1d4c_0
  - numba=0.54.1=py38h4bf6c61_0
  - numpy=1.20.3=py38h9894fe3_1
  - oauth2client=4.1.3=py_0
  - openssl=1.1.1p=h166bdaf_0
  - packaging=21.3=pyhd8ed1ab_0
  - pandas=1.4.0=py38h43a58ef_0
  - parallel=20211222=ha770c72_0
  - paramiko=2.10.3=pyhd8ed1ab_0
  - peppy=0.31.2=pyhd8ed1ab_2
  - perl=5.32.1=1_h7f98852_perl5
  - pip=21.3.1=pyhd8ed1ab_0
  - plac=1.3.5=pyhd8ed1ab_0
  - pluggy=1.0.0=py38h578d9bd_3
  - ply=3.11=py_1
  - prettytable=3.2.0=pyhd8ed1ab_0
  - protobuf=3.20.0=py38hfa26641_4
  - psutil=5.9.0=py38h0a891b7_1
  - pulp=2.6.0=py38h578d9bd_1
  - py=1.11.0=pyh6c4a22f_0
  - pyasn1=0.4.8=py_0
  - pyasn1-modules=0.2.7=py_0
  - pybind11-abi=4=hd8ed1ab_3
  - pycosat=0.6.3=py38h0a891b7_1010
  - pycparser=2.21=pyhd8ed1ab_0
  - pygments=2.11.2=pyhd8ed1ab_0
  - pynacl=1.5.0=py38h0a891b7_1
  - pyopenssl=22.0.0=pyhd8ed1ab_0
  - pyparsing=3.0.8=pyhd8ed1ab_0
  - pyrsistent=0.18.1=py38h0a891b7_1
  - pysftp=0.2.9=py_1
  - pysocks=1.7.1=py38h578d9bd_5
  - pytest=7.1.1=py38h578d9bd_1
  - python=3.8.12=hb7a2778_2_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python-fastjsonschema=2.15.3=pyhd8ed1ab_0
  - python-irodsclient=1.1.3=pyhd8ed1ab_0
  - python_abi=3.8=2_cp38
  - pytz=2021.3=pyhd8ed1ab_0
  - pyu2f=0.1.5=pyhd8ed1ab_0
  - pyyaml=6.0=py38h0a891b7_4
  - ratelimiter=1.2.0=py_1002
  - readline=8.1=h46c0cb4_0
  - reproc=14.2.4=h295c915_1
  - reproc-cpp=14.2.4=h295c915_1
  - requests=2.27.1=pyhd8ed1ab_0
  - retry=0.9.2=py_0
  - rsa=4.8=pyhd8ed1ab_0
  - ruamel_yaml=0.15.100=py38h27cfd23_0
  - rust=1.59.0=h30be4a0_0
  - rust-std-x86_64-unknown-linux-gnu=1.59.0=hc1431ca_0
  - s3transfer=0.5.2=pyhd8ed1ab_0
  - samtools=1.3.1=0
  - scikit-learn=1.0.2=py38h1561384_0
  - scipy=1.7.3=py38h56a6a73_0
  - setuptools=60.9.3=py38h578d9bd_0
  - six=1.16.0=pyh6c4a22f_0
  - slacker=0.14.0=py_0
  - smart_open=5.2.1=pyhd8ed1ab_0
  - smmap=3.0.5=pyh44b312d_0
  - snakemake=7.3.8=hdfd78af_0
  - snakemake-minimal=7.3.8=pyhdfd78af_0
  - sqlite=3.37.0=h9cd32fc_0
  - stone=3.3.1=pyhd8ed1ab_0
  - stopit=1.1.2=py_0
  - sysroot_linux-64=2.12=he073ed8_15
  - tabix=1.11=hdfd78af_0
  - tabixpp=1.1.0=he28291e_6
  - tabulate=0.8.9=pyhd8ed1ab_0
  - threadpoolctl=3.0.0=pyh8a188c0_0
  - tk=8.6.11=h27826a3_1
  - tomli=2.0.1=pyhd8ed1ab_0
  - toposort=1.7=pyhd8ed1ab_0
  - tqdm=4.62.3=pyhd8ed1ab_0
  - traitlets=5.1.1=pyhd8ed1ab_0
  - typing-extensions=4.1.1=hd8ed1ab_0
  - typing_extensions=4.1.1=pyha770c72_0
  - ubiquerg=0.6.1=pyh9f0ad1d_0
  - uritemplate=4.1.1=pyhd8ed1ab_0
  - urllib3=1.26.9=pyhd8ed1ab_0
  - vartrix=1.1.22=h27ee8bf_0
  - vcflib=1.0.2=h3198e80_5
  - veracitools=0.1.3=py_0
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - wheel=0.37.1=pyhd8ed1ab_0
  - wrapt=1.14.0=py38h0a891b7_1
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h7f98852_2
  - yaml-cpp=0.7.0=h27087fc_1
  - yarl=1.7.2=py38h0a891b7_2
  - yte=1.2.1=py38h578d9bd_0
  - zipp=3.8.0=pyhd8ed1ab_0
  - zlib=1.2.11=h36c2ea0_1013
  - zstd=1.5.2=h8a70e8d_1
prefix: /home/rotate/anaconda3/envs/scavengers

  1. After you cloned the repository, you can run scAVENGERS by executing the command below.

$SCAVENGERS_DIRECTORY/scAVENGERS [pipeline|cluster] [options]