From 632777fbd3ebfc7133cb21789151c124e67d9cc6 Mon Sep 17 00:00:00 2001 From: zhangrengang Date: Mon, 18 Sep 2023 13:22:13 +0800 Subject: [PATCH] conda --- OrthoIndex.yaml | 211 ++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 4 +- 2 files changed, 213 insertions(+), 2 deletions(-) create mode 100644 OrthoIndex.yaml diff --git a/OrthoIndex.yaml b/OrthoIndex.yaml new file mode 100644 index 0000000..269f139 --- /dev/null +++ b/OrthoIndex.yaml @@ -0,0 +1,211 @@ +name: OrthoIndex +channels: + - conda-forge + - bioconda +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alsa-lib=1.2.3.2 + - aria2=1.36.0 + - biopython=1.81 + - blast=2.14.1 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - brotli-python=1.1.0 + - bzip2=1.0.8 + - c-ares=1.19.1 + - ca-certificates=2023.7.22 + - certifi=2023.7.22 + - charset-normalizer=3.2.0 + - contourpy=1.1.1 + - curl=7.86.0 + - cycler=0.11.0 + - dbus=1.13.6 + - diamond=2.1.8 + - divvier=1.01 + - drmaa=0.7.9 + - entrez-direct=16.2 + - expat=2.5.0 + - fastme=2.1.6.1 + - fasttree=2.1.11 + - fontconfig=2.14.2 + - fonttools=4.42.1 + - freetype=2.12.1 + - gawk=5.1.0 + - gettext=0.21.1 + - glib=2.68.4 + - glib-tools=2.68.4 + - gmp=6.2.1 + - gst-plugins-base=1.18.5 + - gstreamer=1.18.5 + - icu=68.2 + - idna=3.4 + - importlib-resources=6.0.1 + - importlib_resources=6.0.1 + - iqtree=2.2.5 + - jpeg=9e + - keyutils=1.6.1 + - kiwisolver=1.4.5 + - krb5=1.19.3 + - lazy-property=0.0.1 + - lcms2=2.15 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcblas=3.9.0 + - libclang=11.1.0 + - libcurl=7.86.0 + - libdeflate=1.17 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.10 + - libexpat=2.5.0 + - libffi=3.3 + - libgcc-ng=13.2.0 + - libgfortran-ng=13.2.0 + - libgfortran5=13.2.0 + - libglib=2.68.4 + - libgomp=13.2.0 + - libiconv=1.17 + - libidn2=2.3.4 + - liblapack=3.9.0 + - libllvm11=11.1.0 + - libnghttp2=1.51.0 + - libnsl=2.0.0 + - libogg=1.3.4 + - libopenblas=0.3.24 + - libopus=1.3.1 + - libpng=1.6.39 + - libpq=13.8 + - libsqlite=3.43.0 + - libssh2=1.10.0 + - libstdcxx-ng=13.2.0 + - libtiff=4.5.0 + - libunistring=0.9.10 + - libuuid=2.38.1 + - libvorbis=1.3.7 + - libwebp-base=1.3.2 + - libxcb=1.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.12 + - libzlib=1.2.13 + - mafft=7.520 + - matplotlib=3.7.2 + - matplotlib-base=3.7.2 + - mcl=22.282 + - mmseqs2=14.7e284 + - mpi=1.0 + - munkres=1.1.4 + - muscle=3.8.1551 + - mysql-common=8.0.32 + - mysql-libs=8.0.32 + - ncbi-vdb=3.0.7 + - ncurses=6.4 + - networkx=3.1 + - newick_utils=1.6 + - nspr=4.35 + - nss=3.92 + - numpy=1.24.4 + - openjpeg=2.5.0 + - openmpi=4.1.5 + - openssl=1.1.1w + - orthofinder=2.5.5 + - ossuuid=1.6.2 + - packaging=23.1 + - pal2nal=14.1 + - paml=4.10.6 + - pandas=2.0.3 + - pcre=8.45 + - perl=5.32.1 + - perl-alien-build=2.48 + - perl-alien-libxml2=0.17 + - perl-archive-tar=2.40 + - perl-business-isbn=3.007 + - perl-business-isbn-data=20210112.006 + - perl-capture-tiny=0.48 + - perl-carp=1.50 + - perl-common-sense=3.75 + - perl-compress-raw-bzip2=2.201 + - perl-compress-raw-zlib=2.202 + - perl-constant=1.33 + - perl-encode=3.19 + - perl-exporter=5.74 + - perl-exporter-tiny=1.002002 + - perl-extutils-makemaker=7.70 + - perl-ffi-checklib=0.28 + - perl-file-chdir=0.1011 + - perl-file-path=2.18 + - perl-file-temp=0.2304 + - perl-file-which=1.24 + - perl-getopt-long=2.54 + - perl-importer=0.026 + - perl-io-compress=2.201 + - perl-io-zlib=1.14 + - perl-json=4.10 + - perl-json-xs=2.34 + - perl-list-moreutils=0.430 + - perl-list-moreutils-xs=0.430 + - perl-parent=0.241 + - perl-path-tiny=0.124 + - perl-pathtools=3.75 + - perl-scalar-list-utils=1.63 + - perl-scope-guard=0.21 + - perl-storable=3.15 + - perl-sub-info=0.002 + - perl-term-table=0.016 + - perl-test-fatal=0.016 + - perl-test-warnings=0.031 + - perl-test2-suite=0.000145 + - perl-try-tiny=0.31 + - perl-types-serialiser=1.01 + - perl-uri=5.17 + - perl-xml-libxml=2.0207 + - perl-xml-namespacesupport=1.12 + - perl-xml-sax=1.02 + - perl-xml-sax-base=1.09 + - pillow=9.4.0 + - pip=23.2.1 + - platformdirs=3.10.0 + - pooch=1.7.0 + - psutil=5.9.5 + - pthread-stubs=0.4 + - pyparsing=3.0.9 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtchart=5.12 + - pyqtwebengine=5.12.1 + - pysocks=1.7.1 + - python=3.8.8 + - python-dateutil=2.8.2 + - python-tzdata=2023.3 + - python_abi=3.8 + - pytz=2023.3.post1 + - qt=5.12.9 + - raxml=8.2.12 + - raxml-ng=1.2.0 + - readline=8.2 + - requests=2.31.0 + - scipy=1.10.1 + - setuptools=68.2.2 + - six=1.16.0 + - sqlite=3.43.0 + - tk=8.6.12 + - tornado=6.3.3 + - trimal=1.4.1 + - typing-extensions=4.7.1 + - typing_extensions=4.7.1 + - unicodedata2=15.0.0 + - urllib3=2.0.4 + - wgdi=0.6.5 + - wget=1.20.3 + - wheel=0.41.2 + - xorg-libxau=1.0.11 + - xorg-libxdmcp=1.1.3 + - xz=5.2.6 + - zipp=3.16.2 + - zlib=1.2.13 + - zstd=1.5.5 diff --git a/README.md b/README.md index a3110c0..7a9d54e 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,8 @@ git clone https://github.com/zhangrengang/orthoindex.git cd orthoindex # install -conda env create -f orthoindex.yaml -conda activate orthoindex +conda env create -f OrthoIndex.yaml +conda activate OrthoIndex python3 setup.py install # test