defines explicit conda env using quac v1.0 conda env - closes #49

configs/env/bcftools.yaml

@@ -3,3 +3,32 @@ channels:
   - bioconda
 dependencies:
   - bcftools =1.12
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - gsl=2.6
+  - htslib=1.12
+  - krb5=1.19.2
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.78.0
+  - libdeflate=1.7
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libgcc-ng=11.1.0
+  - libgfortran-ng=11.1.0
+  - libgfortran5=11.1.0
+  - libgomp=11.1.0
+  - libnghttp2=1.43.0
+  - libopenblas=0.3.17
+  - libssh2=1.9.0
+  - libstdcxx-ng=11.1.0
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - perl=5.32.1
+  - tk=8.6.10
+  - xz=5.2.5
+  - zlib=1.2.11

configs/env/covviz.yaml

@@ -5,6 +5,36 @@ channels:
 
 dependencies:
   - python==3.8.5
-  - pip
+  - pip=21.2.3
   - pip:
       - covviz==1.2.2
+  # other dependencies
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - ca-certificates=2021.5.30=ha878542_0
+  - certifi=2021.5.30=py38h578d9bd_0
+  - ld_impl_linux-64=2.36.1=hea4e1c9_2
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=11.1.0=hc902ee8_8
+  - libgomp=11.1.0=hc902ee8_8
+  - libstdcxx-ng=11.1.0=h56837e0_8
+  - ncurses=6.2=h58526e2_4
+  - openssl=1.1.1k=h7f98852_0
+  - python_abi=3.8=2_cp38
+  - readline=8.1=h46c0cb4_0
+  - setuptools=49.6.0=py38h578d9bd_3
+  - sqlite=3.36.0=h9cd32fc_0
+  - tk=8.6.10=h21135ba_1
+  - wheel=0.37.0=pyhd8ed1ab_0
+  - xz=5.2.5=h516909a_1
+  - zlib=1.2.11=h516909a_1010
+  - pip:
+      - future==0.18.2
+      - jinja2==3.0.1
+      - lzstring==1.0.4
+      - markupsafe==2.0.1
+      - numpy==1.21.1
+      - pandas==1.3.1
+      - python-dateutil==2.8.2
+      - pytz==2021.1
+      - six==1.16.0

configs/env/goleft.yaml

@@ -3,3 +3,26 @@ channels:
   - bioconda
 dependencies:
   - goleft ==0.2.4
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - htslib=1.13
+  - krb5=1.19.2
+  - libcurl=7.78.0
+  - libdeflate=1.7
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libgcc-ng=11.1.0
+  - libgomp=11.1.0
+  - libnghttp2=1.43.0
+  - libssh2=1.9.0
+  - libstdcxx-ng=11.1.0
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - samtools=1.13
+  - tk=8.6.10
+  - xz=5.2.5
+  - zlib=1.2.11

configs/env/mosdepth.yaml

@@ -6,3 +6,26 @@ channels:
 
 dependencies:
   - mosdepth==0.3.1
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - htslib=1.12
+  - krb5=1.19.2
+  - libcurl=7.78.0
+  - libdeflate=1.7
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libgcc-ng=11.1.0
+  - libgomp=11.1.0
+  - libnghttp2=1.43.0
+  - libssh2=1.9.0
+  - libstdcxx-ng=11.1.0
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - pcre=8.45
+  - tk=8.6.10
+  - xz=5.2.5
+  - zlib=1.2.11

configs/env/multiqc.yaml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   - python=3.6.13
   - multiqc==1.9
+  # other dependencies
   - networkx=2.5
   - numpy=1.19.5
   - _libgcc_mutex=0.1

configs/env/picard.yaml

@@ -8,3 +8,106 @@ dependencies:
   - picard==2.23.0
   - openjdk==11.0.9.1
   - r-base==4.0.3
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.1
+  - alsa-lib=1.2.3
+  - binutils_impl_linux-64=2.36.1
+  - binutils_linux-64=2.36
+  - bwidget=1.9.14
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - cairo=1.16.0
+  - curl=7.76.1
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.13.1
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - freetype=2.10.4
+  - fribidi=1.0.10
+  - gcc_impl_linux-64=9.4.0
+  - gcc_linux-64=9.4.0
+  - gettext=0.19.8.1
+  - gfortran_impl_linux-64=9.4.0
+  - gfortran_linux-64=9.4.0
+  - giflib=5.2.1
+  - graphite2=1.3.13
+  - gsl=2.6
+  - gxx_impl_linux-64=9.4.0
+  - gxx_linux-64=9.4.0
+  - harfbuzz=2.8.2
+  - icu=68.1
+  - jbig=2.1
+  - jpeg=9d
+  - kernel-headers_linux-64=2.6.32
+  - krb5=1.17.2
+  - lcms2=2.12
+  - ld_impl_linux-64=2.36.1
+  - lerc=2.2.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.76.1
+  - libdeflate=1.7
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libffi=3.3
+  - libgcc-devel_linux-64=9.4.0
+  - libgcc-ng=11.1.0
+  - libgfortran-ng=11.1.0
+  - libgfortran5=11.1.0
+  - libglib=2.68.3
+  - libgomp=11.1.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libnghttp2=1.43.0
+  - libopenblas=0.3.17
+  - libpng=1.6.37
+  - libsanitizer=9.4.0
+  - libssh2=1.9.0
+  - libstdcxx-devel_linux-64=9.4.0
+  - libstdcxx-ng=11.1.0
+  - libtiff=4.3.0
+  - libuuid=2.32.1
+  - libwebp-base=1.2.0
+  - libxcb=1.13
+  - libxml2=2.9.12
+  - lz4-c=1.9.3
+  - make=4.3
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - pango=1.48.7
+  - pcre=8.45
+  - pcre2=10.36
+  - pixman=0.40.0
+  - pthread-stubs=0.4
+  - readline=8.1
+  - sed=4.8
+  - sysroot_linux-64=2.12
+  - tk=8.6.10
+  - tktable=2.10
+  - xorg-fixesproto=5.0
+  - xorg-inputproto=2.3.2
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.7.2
+  - xorg-libxau=1.0.9
+  - xorg-libxdmcp=1.1.3
+  - xorg-libxext=1.3.4
+  - xorg-libxfixes=5.0.3
+  - xorg-libxi=1.7.10
+  - xorg-libxrender=0.9.10
+  - xorg-libxt=1.2.1
+  - xorg-libxtst=1.2.3
+  - xorg-recordproto=1.14.2
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.5
+  - zlib=1.2.11
+  - zstd=1.5.0

configs/env/quac_watch.yaml

@@ -3,9 +3,87 @@ channels:
   - anaconda
   - bioconda
 dependencies:
-  - python =3.6
-  - pandas =1.1
+  - python=3.6.13
+  - pandas=1.1.5
+  - numpy=1.19.5
   - jinja2==2.11.3
   - pyyaml=5.3
   - fire=0.3
   - multiqc=1.9
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - brotlipy=0.7.0
+  - ca-certificates=2021.5.30
+  - certifi=2021.5.30
+  - cffi=1.14.6
+  - chardet=4.0.0
+  - charset-normalizer=2.0.0
+  - click=8.0.1
+  - coloredlogs=15.0.1
+  - colormath=3.0.0
+  - cryptography=3.4.7
+  - cycler=0.10.0
+  - decorator=5.0.9
+  - freetype=2.10.4
+  - future=0.18.2
+  - humanfriendly=9.2
+  - idna=3.1
+  - importlib-metadata=4.6.3
+  - jbig=2.1
+  - jpeg=9d
+  - kiwisolver=1.3.1
+  - lcms2=2.12
+  - ld_impl_linux-64=2.36.1
+  - lerc=2.2.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libdeflate=1.7
+  - libffi=3.3
+  - libgcc-ng=11.1.0
+  - libgfortran-ng=11.1.0
+  - libgfortran5=11.1.0
+  - libgomp=11.1.0
+  - liblapack=3.9.0
+  - libopenblas=0.3.17
+  - libpng=1.6.37
+  - libstdcxx-ng=11.1.0
+  - libtiff=4.3.0
+  - libwebp-base=1.2.0
+  - lz4-c=1.9.3
+  - lzstring=1.0.4
+  - markdown=3.3.4
+  - markupsafe=2.0.1
+  - matplotlib-base=3.3.4
+  - ncurses=6.2
+  - networkx=2.5
+  - olefile=0.46
+  - openjpeg=2.4.0
+  - openssl=1.1.1k
+  - pillow=8.3.1
+  - pip=21.2.3
+  - pycparser=2.20
+  - pyopenssl=20.0.1
+  - pyparsing=2.4.7
+  - pysocks=1.7.1
+  - python-dateutil=2.8.2
+  - python_abi=3.6
+  - pytz=2021.1
+  - readline=8.1
+  - requests=2.26.0
+  - setuptools=49.6.0
+  - simplejson=3.17.3
+  - six=1.16.0
+  - spectra=0.0.11
+  - sqlite=3.36.0
+  - termcolor=1.1.0
+  - tk=8.6.10
+  - tornado=6.1
+  - typing_extensions=3.10.0.0
+  - urllib3=1.26.6
+  - wheel=0.37.0
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zipp=3.5.0
+  - zlib=1.2.11
+  - zstd=1.5.0

configs/env/qualimap.yaml

-
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - qualimap =2.2
+  - qualimap ==2.2.2d
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.1
+  - alsa-lib=1.2.3
+  - binutils_impl_linux-64=2.36.1
+  - binutils_linux-64=2.36
+  - bioconductor-biobase=2.52.0
+  - bioconductor-biocgenerics=0.38.0
+  - bioconductor-biocio=1.2.0
+  - bioconductor-biocparallel=1.26.0
+  - bioconductor-biostrings=2.60.0
+  - bioconductor-delayedarray=0.18.0
+  - bioconductor-genomeinfodb=1.28.0
+  - bioconductor-genomeinfodbdata=1.2.6
+  - bioconductor-genomicalignments=1.28.0
+  - bioconductor-genomicranges=1.44.0
+  - bioconductor-iranges=2.26.0
+  - bioconductor-matrixgenerics=1.4.0
+  - bioconductor-noiseq=2.36.0
+  - bioconductor-rhtslib=1.24.0
+  - bioconductor-rsamtools=2.8.0
+  - bioconductor-rtracklayer=1.52.0
+  - bioconductor-s4vectors=0.30.0
+  - bioconductor-summarizedexperiment=1.22.0
+  - bioconductor-xvector=0.32.0
+  - bioconductor-zlibbioc=1.38.0
+  - bwidget=1.9.14
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - cairo=1.16.0
+  - curl=7.78.0
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.13.1
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - freetype=2.10.4
+  - fribidi=1.0.10
+  - gcc_impl_linux-64=9.4.0
+  - gcc_linux-64=9.4.0
+  - gettext=0.19.8.1
+  - gfortran_impl_linux-64=9.4.0
+  - gfortran_linux-64=9.4.0
+  - giflib=5.2.1
+  - graphite2=1.3.13
+  - gsl=2.6
+  - gxx_impl_linux-64=9.4.0
+  - gxx_linux-64=9.4.0
+  - harfbuzz=2.8.2
+  - icu=68.1
+  - jbig=2.1
+  - jpeg=9d
+  - kernel-headers_linux-64=2.6.32
+  - krb5=1.19.2
+  - lcms2=2.12
+  - ld_impl_linux-64=2.36.1
+  - lerc=2.2.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=7.78.0
+  - libdeflate=1.7
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libffi=3.3
+  - libgcc-devel_linux-64=9.4.0
+  - libgcc-ng=11.1.0
+  - libgfortran-ng=11.1.0
+  - libgfortran5=11.1.0
+  - libglib=2.68.3
+  - libgomp=11.1.0
+  - libiconv=1.16
+  - liblapack=3.9.0
+  - libnghttp2=1.43.0
+  - libopenblas=0.3.17
+  - libpng=1.6.37
+  - libsanitizer=9.4.0
+  - libssh2=1.9.0
+  - libstdcxx-devel_linux-64=9.4.0
+  - libstdcxx-ng=11.1.0
+  - libtiff=4.3.0
+  - libuuid=2.32.1
+  - libwebp-base=1.2.0
+  - libxcb=1.13
+  - libxml2=2.9.12
+  - lz4-c=1.9.3
+  - make=4.3
+  - ncurses=6.2
+  - openjdk=11.0.9.1
+  - openssl=1.1.1k
+  - pango=1.48.7
+  - pcre=8.45
+  - pcre2=10.37
+  - pixman=0.40.0
+  - pthread-stubs=0.4
+  - r-base=4.1.1
+  - r-bh=1.75.0_0
+  - r-bitops=1.0_7
+  - r-crayon=1.4.1
+  - r-formatr=1.11
+  - r-futile.logger=1.4.3
+  - r-futile.options=1.0.1
+  - r-getopt=1.20.3
+  - r-lambda.r=1.2.4
+  - r-lattice=0.20_44
+  - r-matrix=1.3_4
+  - r-matrixstats=0.60.0
+  - r-optparse=1.6.6
+  - r-rcurl=1.98_1.3
+  - r-restfulr=0.0.13
+  - r-rjson=0.2.20
+  - r-snow=0.4_3
+  - r-xml=3.99_0.6
+  - r-yaml=2.2.1
+  - readline=8.1
+  - sed=4.8
+  - sysroot_linux-64=2.12
+  - tk=8.6.10
+  - tktable=2.10
+  - xorg-fixesproto=5.0
+  - xorg-inputproto=2.3.2
+  - xorg-kbproto=1.0.7
+  - xorg-libice=1.0.10
+  - xorg-libsm=1.2.3
+  - xorg-libx11=1.7.2
+  - xorg-libxau=1.0.9
+  - xorg-libxdmcp=1.1.3
+  - xorg-libxext=1.3.4
+  - xorg-libxfixes=5.0.3
+  - xorg-libxi=1.7.10
+  - xorg-libxrender=0.9.10
+  - xorg-libxt=1.2.1
+  - xorg-libxtst=1.2.3
+  - xorg-recordproto=1.14.2
+  - xorg-renderproto=0.11.1
+  - xorg-xextproto=7.3.0
+  - xorg-xproto=7.0.31
+  - xz=5.2.5
+  - zlib=1.2.11
+  - zstd=1.5.0

configs/env/verifyBamID.yaml

@@ -7,3 +7,27 @@ channels:
 dependencies:
   - verifybamid2==2.0.1
   - htslib==1.10.2
+  # other dependencies
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - c-ares=1.17.2
+  - ca-certificates=2021.5.30
+  - curl=7.78.0
+  - htslib=1.10.2
+  - krb5=1.19.2
+  - libcurl=7.78.0
+  - libdeflate=1.6
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libgcc-ng=11.1.0
+  - libgomp=11.1.0
+  - libnghttp2=1.43.0
+  - libssh2=1.9.0
+  - libstdcxx-ng=11.1.0
+  - ncurses=6.2
+  - openssl=1.1.1k
+  - tk=8.6.10
+  - verifybamid2=2.0.1
+  - xz=5.2.5
+  - zlib=1.2.11