BOL: Set up WGD environment using conda !

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BioStar
Set up WGD environment using conda !
Set up WGD environment using conda !

By BioStar 1395 days ago
#Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, because it #depends on a lot of software. wgd depends on the following software

#BLAST
#MCL
#MUSCLE/MAFFT/PRANK
#PAML
#PhyML/FastTree
#i-ADHoRe

#Creat the conda ENV and install its deps
#Follow the steps
(base) ➜  wgd git:(master)  conda create -n wgd python=3.7 blast mcl muscle mafft prank paml  fasttree cmake libpng mpi=1.0=mpich
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.0
  latest version: 4.9.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/anaconda3/envs/wgd

  added / updated specs:
    - blast
    - cmake
    - fasttree
    - libpng
    - mafft
    - mcl
    - mpi==1.0=mpich
    - muscle
    - paml
    - prank
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    boost-1.74.0               |   py37he5a615d_2         335 KB  conda-forge
    boost-cpp-1.74.0           |       h9d3c048_1        16.3 MB  conda-forge
    c-ares-1.17.1              |       h36c2ea0_0         111 KB  conda-forge
    certifi-2020.12.5          |   py37h89c1867_1         143 KB  conda-forge
    cmake-3.19.3               |       h4547794_0        14.0 MB  conda-forge
    libblas-3.9.0              |       7_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       7_openblas          11 KB  conda-forge
    libgfortran-ng-9.3.0       |      hff62375_18          22 KB  conda-forge
    libgfortran5-9.3.0         |      hff62375_18         2.0 MB  conda-forge
    liblapack-3.9.0            |       7_openblas          11 KB  conda-forge
    libnghttp2-1.41.0          |       h8cfc5f6_2         774 KB  conda-forge
    numpy-1.19.5               |   py37haa41c4c_1         5.3 MB  conda-forge
    python-3.7.9               |hffdb5ce_0_cpython        57.3 MB  conda-forge
    setuptools-49.6.0          |   py37h89c1867_3         947 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        97.2 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  blast              bioconda/linux-64::blast-2.5.0-hc0b0e79_3
  boost              conda-forge/linux-64::boost-1.74.0-py37he5a615d_2
  boost-cpp          conda-forge/linux-64::boost-cpp-1.74.0-h9d3c048_1
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h36c2ea0_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
  cmake              conda-forge/linux-64::cmake-3.19.3-h4547794_0
  expat              conda-forge/linux-64::expat-2.2.9-he1b5a44_2
  fasttree           bioconda/linux-64::fasttree-2.1.10-h516909a_4
  icu                conda-forge/linux-64::icu-68.1-h58526e2_0
  krb5               conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_1
  libblas            conda-forge/linux-64::libblas-3.9.0-7_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-7_openblas
  libcurl            conda-forge/linux-64::libcurl-7.71.1-hcdd3856_8
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_18
  libgfortran5       conda-forge/linux-64::libgfortran5-9.3.0-hff62375_18
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
  liblapack          conda-forge/linux-64::liblapack-3.9.0-7_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.41.0-h8cfc5f6_2
  libopenblas        conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1
  libpng             conda-forge/linux-64::libpng-1.6.37-h21135ba_2
  libssh2            conda-forge/linux-64::libssh2-1.9.0-hab1572f_5
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
  libuv              conda-forge/linux-64::libuv-1.40.0-h7f98852_0
  lz4-c              conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0
  mafft              bioconda/linux-64::mafft-7.475-h516909a_0
  mcl                bioconda/linux-64::mcl-14.137-pl526h516909a_5
  mpi                conda-forge/linux-64::mpi-1.0-mpich
  muscle             bioconda/linux-64::muscle-3.8.1551-hc9558a2_5
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  numpy              conda-forge/linux-64::numpy-1.19.5-py37haa41c4c_1
  openssl            conda-forge/linux-64::openssl-1.1.1i-h7f98852_0
  paml               bioconda/linux-64::paml-4.9-h516909a_5
  perl               conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
  pip                conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0
  prank              bioconda/linux-64::prank-v.170427-hc9558a2_3
  python             conda-forge/linux-64::python-3.7.9-hffdb5ce_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  rhash              conda-forge/linux-64::rhash-1.4.1-h7f98852_0
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
  sqlite             conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010
  zstd               conda-forge/linux-64::zstd-1.4.8-ha95c52a_1


Proceed ([y]/n)? y


Downloading and Extracting Packages
libgfortran-ng-9.3.0 | 22 KB     | ################################################################################ | 100%
libnghttp2-1.41.0    | 774 KB    | ################################################################################ | 100%
libcblas-3.9.0       | 11 KB     | ################################################################################ | 100%
liblapack-3.9.0      | 11 KB     | ################################################################################ | 100%
certifi-2020.12.5    | 143 KB    | ################################################################################ | 100%
cmake-3.19.3         | 14.0 MB   | ################################################################################ | 100%
libgfortran5-9.3.0   | 2.0 MB    | ################################################################################ | 100%
c-ares-1.17.1        | 111 KB    | ################################################################################ | 100%
numpy-1.19.5         | 5.3 MB    | ################################################################################ | 100%
libblas-3.9.0        | 11 KB     | ################################################################################ | 100%
python-3.7.9         | 57.3 MB   | ################################################################################ | 100%
boost-cpp-1.74.0     | 16.3 MB   | ################################################################################ | 100%
setuptools-49.6.0    | 947 KB    | ################################################################################ | 100%
boost-1.74.0         | 335 KB    | ################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate wgd
#
# To deactivate an active environment, use
#
#     $ conda deactivate




#----------------------------------------------------- set uo wgd

(wgd) ➜  Tools git:(master) ✗ git clone https://github.com/arzwa/wgd.git
(wgd) ➜  Tools git:(master) ✗ cd wgd
(wgd) ➜  wgd git:(master) ls
doc  example  LICENSE  README.md  setup.py  Singularity  wgd  wgd_cli.py
(wgd) ➜  wgd git:(master) pip install .
Processing /home/urbe/Tools/wgd
Requirement already satisfied: numpy>=1.16 in /home/urbe/anaconda3/envs/wgd/lib/python3.7/site-packages (from wgd==1.2) (1.19.5)
Collecting bokeh==1.4.0
  Using cached bokeh-1.4.0.tar.gz (32.4 MB)
Collecting fastcluster==1.1.25
  Downloading fastcluster-1.1.25-cp37-cp37m-manylinux1_x86_64.whl (154 kB)
     |████████████████████████████████| 154 kB 5.8 MB/s
Collecting joblib==0.11
  Using cached joblib-0.11-py2.py3-none-any.whl (176 kB)
Collecting pandas==0.24.1
  Downloading pandas-0.24.1-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB)
     |████████████████████████████████| 10.1 MB 29 kB/s
Collecting biopython>=1.75
  Using cached biopython-1.78-cp37-cp37m-manylinux1_x86_64.whl (2.3 MB)
Collecting click>=7.0
  Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting coloredlogs>=10.0
  Using cached coloredlogs-15.0-py2.py3-none-any.whl (45 kB)
Collecting ete3>=3.1
  Using cached ete3-3.1.2.tar.gz (4.7 MB)
Collecting humanfriendly>=9.1
  Using cached humanfriendly-9.1-py2.py3-none-any.whl (86 kB)
Collecting Jinja2>=2.7
  Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting MarkupSafe>=0.23
  Using cached MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB)
Collecting matplotlib>=3.0.2
  Downloading matplotlib-3.3.3-cp37-cp37m-manylinux1_x86_64.whl (11.6 MB)
     |████████████████████████████████| 11.6 MB 29 kB/s
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.1-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB)
     |████████████████████████████████| 1.1 MB 68.0 MB/s
Collecting packaging>=16.8
  Using cached packaging-20.8-py2.py3-none-any.whl (39 kB)
Collecting pillow>=4.0
  Downloading Pillow-8.1.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB)
     |████████████████████████████████| 2.2 MB 53.5 MB/s
Collecting plumbum>=1.6.7
  Using cached plumbum-1.6.9-py2.py3-none-any.whl (115 kB)
Collecting progressbar2>=3.39
  Using cached progressbar2-3.53.1-py2.py3-none-any.whl (25 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting python-utils>=2.3.0
  Downloading python_utils-2.5.1-py2.py3-none-any.whl (13 kB)
Collecting pytz>=2011k
  Downloading pytz-2020.5-py2.py3-none-any.whl (510 kB)
     |████████████████████████████████| 510 kB 38.1 MB/s
Collecting PyYAML>=3.10
  Using cached PyYAML-5.3.1.tar.gz (269 kB)
Collecting scipy>=1.2
  Downloading scipy-1.6.0-cp37-cp37m-manylinux1_x86_64.whl (27.4 MB)
     |████████████████████████████████| 27.4 MB 2.0 kB/s
Collecting seaborn>=0.9.0
  Using cached seaborn-0.11.1-py3-none-any.whl (285 kB)
Collecting six>=1.5.2
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting tornado>=4.3
  Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB)
     |████████████████████████████████| 428 kB 61.8 MB/s
Collecting sklearn
  Using cached sklearn-0.0.tar.gz (1.1 kB)
Collecting scikit-learn
  Downloading scikit_learn-0.24.0-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB)
     |████████████████████████████████| 22.3 MB 6.0 kB/s
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Building wheels for collected packages: wgd, bokeh, ete3, PyYAML, sklearn
  Building wheel for wgd (setup.py) ... done
  Created wheel for wgd: filename=wgd-1.2-py3-none-any.whl size=75291 sha256=56a7a19b3f4e535897038e8297166a640a7a6a7fdfeb89f5afde4aaa0208ae67
  Stored in directory: /tmp/pip-ephem-wheel-cache-29m8tx5i/wheels/54/f3/0c/285aa1e33c52ac42d7996c0170a686e47362e33f012b2b3669
  Building wheel for bokeh (setup.py) ... done
  Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689200 sha256=7daa115fd1b052d429abb6c7082cbbb96defc81716da99ce873760cedf0dbe6f
  Stored in directory: /home/urbe/.cache/pip/wheels/49/8c/d1/6b8e1f57e542671673cb3d2faee1a9eccb36be2c08a3915498
  Building wheel for ete3 (setup.py) ... done
  Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2272998 sha256=4f8c179d7e30d22661fff06e2be08125d837dcff31d4eac36dfb206639ce693f
  Stored in directory: /home/urbe/.cache/pip/wheels/17/fd/e2/6ac384d8c2484789304657dde01b96d7ab83f4f1dd96d266df
  Building wheel for PyYAML (setup.py) ... done
  Created wheel for PyYAML: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=89175438317c730e5db0088255ca2f5a9745368487ed0fd0c7dbf644774c45c0
  Stored in directory: /home/urbe/.cache/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653
  Building wheel for sklearn (setup.py) ... done
  Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1316 sha256=4e2eed235501a23fa4cb58a4faef00b3c824d88a5a6d6b7478d45bdfd09bad6c
  Stored in directory: /home/urbe/.cache/pip/wheels/46/ef/c3/157e41f5ee1372d1be90b09f74f82b10e391eaacca8f22d33e
Successfully built wgd bokeh ete3 PyYAML sklearn
Installing collected packages: six, threadpoolctl, scipy, pytz, python-dateutil, pyparsing, pillow, MarkupSafe, kiwisolver, joblib, cycler, tornado, scikit-learn, PyYAML, python-utils, pandas, packaging, matplotlib, Jinja2, humanfriendly, sklearn, seaborn, progressbar2, plumbum, fastcluster, ete3, coloredlogs, click, bokeh, biopython, wgd
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 PyYAML-5.3.1 biopython-1.78 bokeh-1.4.0 click-7.1.2 coloredlogs-15.0 cycler-0.10.0 ete3-3.1.2 fastcluster-1.1.25 humanfriendly-9.1 joblib-0.11 kiwisolver-1.3.1 matplotlib-3.3.3 packaging-20.8 pandas-0.24.1 pillow-8.1.0 plumbum-1.6.9 progressbar2-3.53.1 pyparsing-2.4.7 python-dateutil-2.8.1 python-utils-2.5.1 pytz-2020.5 scikit-learn-0.24.0 scipy-1.6.0 seaborn-0.11.1 six-1.15.0 sklearn-0.0 threadpoolctl-2.1.0 tornado-6.1 wgd-1.2

(wgd) ➜  wgd git:(master) wgd
zsh: correct 'wgd' to 'gd' [nyae]? n
Usage: wgd [OPTIONS] COMMAND [ARGS]...

  Welcome to the wgd command line interface!

                         _______
                         \  ___ `'.
         _     _ .--./)   ' |--.\  \
   /\    \\   ///.''\\    | |    \  '
   `\\  //\\ //| |  | |   | |     |  '
     \`//  \'/  \`-' /    | |     |  |
      \|   |/   /("'`     | |     ' .'
       '        \ '---.   | |___.' /'
                 /'""'.\ /_______.'/
                ||     ||\_______|/
                \'. __//
                 `'---'

  wgd  Copyright (C) 2018 Arthur Zwaenepoel
  This program comes with ABSOLUTELY NO WARRANTY;
  This is free software, and you are welcome to redistribute it
  under certain conditions;

  Contact: arzwa@psb.vib-ugent.be

Options:
  -v, --verbosity [info|debug]  Verbosity level, default = info.
  -l, --logfile TEXT            File to write logs to (optional)
  --version                     Print version number
  -h, --help                    Show this message and exit.

Commands:
  dmd  All-vs.-all diamond blastp + MCL clustering.
  kde  Fit a KDE to a Ks distribution.
  ksd  Ks distribution construction.
  mcl  All-vs.-all blastp + MCL clustering.
  mix  Mixture modeling of Ks distributions.
  pre  Check and optionally rename CDS files.
  syn  Co-linearity analyses.
  viz  Plot histograms/densities (interactively).
  wf1  Standard workflow whole paranome Ks.
  wf2  Standard workflow one-vs-one ortholog Ks.
BOL

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Set up WGD environment using conda !
