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/v0.2.0.tar.gz
tar -xvzf v0.2.0.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