updated PlasFlow YAML (issue #20)

envs/PlasFlow.yaml

-name: Plasmid
 channels:
-  - jjhelmus
-  - bioconda/label/cf201901
-  - conda-forge
+  # for PlasFlow
+  - smaegol
+  # rest
   - bioconda
+  - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_llvm
   - _r-mutex=1.0.1=anacondar_1
-  - absl-py=0.5.0=py_0
-  - astor=0.7.1=py_0
-  - bioconductor-biocgenerics=0.26.0=r341_0
-  - bioconductor-biostrings=2.48.0=r341h470a237_0
-  - bioconductor-iranges=2.14.12=r341h470a237_0
-  - bioconductor-s4vectors=0.18.3=r341h470a237_0
-  - bioconductor-xvector=0.20.0=r341h470a237_0
-  - bioconductor-zlibbioc=1.26.0=r341h470a237_0
-  - biopython=1.72=py35_0
-  - blas=2.12=openblas
-  - bzip2=1.0.8=h516909a_0
-  - c-ares=1.15.0=h516909a_1001
-  - ca-certificates=2019.6.16=hecc5488_0
-  - cairo=1.14.12=h80bd089_1005
+  - backports=1.0=py_2
+  - backports.weakref=1.0rc1=py35_1
+  - bioconductor-biocgenerics=0.22.0=r3.3.2_0
+  - bioconductor-biostrings=2.42.1=r3.3.2_0
+  - bioconductor-iranges=2.8.2=r3.3.2_0
+  - bioconductor-s4vectors=0.12.2=r3.3.2_0
+  - bioconductor-xvector=0.14.1=r3.3.2_0
+  - bioconductor-zlibbioc=1.20.0=r3.3.2_1
+  - biopython=1.68=py35_0
+  - blas=2.16=openblas
+  - bleach=1.5.0=py35_0
+  - bzip2=1.0.8=h516909a_2
+  - ca-certificates=2020.4.5.1=hecc5488_0
+  - cairo=1.14.6=4
   - certifi=2018.8.24=py35_1001
-  - curl=7.61.0=h93b3f91_2
-  - fontconfig=2.13.1=he4413a7_1000
-  - freetype=2.10.0=he983fc9_1
-  - gast=0.2.2=py_0
+  - curl=7.52.1=0
+  - fontconfig=2.12.1=6
+  - freetype=2.7=1
   - gettext=0.19.8.1=hc5be6a0_1002
-  - glib=2.56.2=had28632_1001
-  - graphite2=1.3.13=hf484d3e_1000
-  - grpcio=1.14.1=py35hd60e7a3_0
-  - gsl=2.2.1=h0c605f7_3
-  - harfbuzz=1.9.0=he243708_1001
+  - glib=2.51.4=0
+  - graphite2=1.3.13=he1b5a44_1001
+  - gsl=2.6=h294904e_0
+  - harfbuzz=1.4.3=0
+  - html5lib=0.9999999=py35_0
   - icu=58.2=hf484d3e_1000
   - jpeg=9c=h14c3975_1001
-  - krb5=1.14.6=0
-  - libblas=3.8.0=12_openblas
-  - libcblas=3.8.0=12_openblas
-  - libffi=3.2.1=he1b5a44_1006
+  - libblas=3.8.0=16_openblas
+  - libcblas=3.8.0=16_openblas
+  - libffi=3.2.1=he1b5a44_1007
   - libgcc=7.2.0=h69d50b8_2
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran=3.0.0=1
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - libiconv=1.15=h516909a_1005
-  - liblapack=3.8.0=12_openblas
-  - liblapacke=3.8.0=12_openblas
-  - libopenblas=0.3.7=h6e990d7_1
-  - libpng=1.6.37=hed695b0_0
-  - libprotobuf=3.6.0=hdbcaa40_1000
-  - libssh2=1.8.0=h1ad7b7a_1003
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - libtiff=4.0.10=h57b8799_1003
-  - libuuid=2.32.1=h14c3975_1000
-  - libxcb=1.13=h14c3975_1002
-  - libxml2=2.9.9=h13577e0_2
-  - lz4-c=1.8.3=he1b5a44_1001
-  - markdown=3.1.1=py_0
+  - libgcc-ng=9.2.0=h24d8f2e_2
+  - libgfortran-ng=7.3.0=hdf63c60_5
+  - libiconv=1.15=h516909a_1006
+  - liblapack=3.8.0=16_openblas
+  - liblapacke=3.8.0=16_openblas
+  - libopenblas=0.3.9=h5ec1e0e_0
+  - libpng=1.6.28=1
+  - libstdcxx-ng=9.2.0=hdf63c60_2
+  - libtiff=4.0.7=0
+  - libxml2=2.9.5=0
+  - llvm-openmp=10.0.0=hc9558a2_0
+  - markdown=3.2.1=py_0
+  - mmtf-python=1.0.2=py35_0
   - mock=2.0.0=py35_0
-  - ncurses=6.1=hf484d3e_1002
+  - msgpack-python=0.5.6=py35h2d50403_3
+  - ncurses=5.9=10
   - numpy=1.15.2=py35h99e49ec_0
   - numpy-base=1.15.2=py35h2f8d375_0
-  - openssl=1.0.2r=h14c3975_0
+  - olefile=0.46=py_0
+  - openssl=1.0.2u=h516909a_0
   - pandas=0.23.4=py35hf8a1672_0
-  - pango=1.40.14=hf0c64fd_1003
+  - pango=1.40.4=0
   - pbr=5.4.2=py_0
-  - pcre=8.41=hf484d3e_1003
-  - perl=5.26.2=h516909a_1006
-  - perl-bioperl=1.6.924=4
-  - perl-getopt-long=2.50=pl526_1
-  - perl-threaded=5.26.0=0
-  - perl-yaml=1.29=pl526_0
-  - pip=18.0=py35_1001
+  - pcre=8.44=he1b5a44_0
+  - pillow=4.3.0=py35_0
+  - pip=20.0.2=py_2
   - pixman=0.34.0=h14c3975_1003
-  - protobuf=3.0.0b2=py35_1
-  - pthread-stubs=0.4=h14c3975_1001
-  - python=3.5.5=h5001a0f_2
-  - python-dateutil=2.8.0=py_0
-  - pytz=2019.2=py_0
-  - r-base=3.4.1=h4fe35fd_8
-  - readline=7.0=hf8c457e_1001
-  - rpy2=2.8.5=py35r3.4.1_0
+  - protobuf=3.4.0=py35_0
+  - python=3.5.4=0
+  - python-dateutil=2.8.1=py_0
+  - pytz=2019.3=py_0
+  - r-base=3.3.2=5
+  - readline=6.2=0
+  - reportlab=3.4.0=py35_0
+  - rpy2=2.7.8=py35r3.3.2_1
   - scikit-learn=0.20.0=py35h22eb022_1
   - scipy=1.1.0=py35he2b7bc3_1
   - setuptools=40.4.3=py35_0
-  - six=1.11.0=py35_1
-  - sqlite=3.28.0=h8b20d00_0
-  - tensorflow=0.10.0rc0=py35_1
-  - termcolor=1.1.0=py_2
-  - tk=8.6.9=hed695b0_1002
-  - werkzeug=0.15.5=py_0
-  - wheel=0.32.0=py35_1000
-  - xorg-kbproto=1.0.7=h14c3975_1002
-  - xorg-libice=1.0.10=h516909a_0
-  - xorg-libsm=1.2.3=h84519dc_1000
-  - xorg-libx11=1.6.8=h516909a_0
-  - xorg-libxau=1.0.9=h14c3975_0
-  - xorg-libxdmcp=1.1.3=h516909a_0
-  - xorg-libxext=1.3.4=h516909a_0
-  - xorg-libxrender=0.9.10=h516909a_1002
-  - xorg-libxt=1.2.0=h516909a_0
-  - xorg-renderproto=0.11.1=h14c3975_1002
-  - xorg-xextproto=7.3.0=h14c3975_1002
-  - xorg-xproto=7.0.31=h14c3975_1007
-  - xz=5.2.4=h14c3975_1001
-  - zlib=1.2.11=h516909a_1005
-  - zstd=1.4.0=h3b9ef0a_0
-  - pip:
-    - plasflow==1.1.0
-prefix: /home/users/ldenies/apps/miniconda3/envs/PlasFlow
+  - six=1.14.0=py_1
+  - sqlite=3.13.0=1
+  - tensorflow=1.3.0=py35_0
+  - tk=8.5.19=2
+  - webencodings=0.5.1=py_1
+  - werkzeug=1.0.1=pyh9f0ad1d_0
+  - wheel=0.34.2=py_1
+  - xz=5.2.5=h516909a_0
+  - zlib=1.2.8=3
+  # PlasFlow: should be installed from smaegol, NOT from pip
+  - plasflow=1.1.0