Created
May 1, 2019 12:07
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Conda env config file for PacBio full-length transcriptome sequencing analysis
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| name: anaCogent5.2 | |
| channels: | |
| - bioconda | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ | |
| - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ | |
| - defaults | |
| dependencies: | |
| - _r-mutex=1.0.0=anacondar_1 | |
| - alabaster=0.7.12=py27_0 | |
| - anaconda=custom=py27h4a00acb_0 | |
| - anaconda-client=1.7.2=py27_0 | |
| - anaconda-project=0.8.2=py27_0 | |
| - asn1crypto=0.24.0=py27_0 | |
| - astroid=1.6.5=py27_0 | |
| - astropy=2.0.7=py27h3010b51_1 | |
| - atomicwrites=1.2.1=py27_0 | |
| - attrs=18.2.0=py27h28b3542_0 | |
| - avro=1.8.0=py27_0 | |
| - babel=2.6.0=py27_0 | |
| - backports=1.0=py27_1 | |
| - backports.functools_lru_cache=1.5=py27_1 | |
| - backports.os=0.1.1=py27_0 | |
| - backports.shutil_get_terminal_size=1.0.0=py27_2 | |
| - backports_abc=0.5=py27h7b3c97b_0 | |
| - bcftools=1.9=h47928c2_1 | |
| - beautifulsoup4=4.6.3=py27_0 | |
| - binutils_impl_linux-64=2.31.1=h6176602_1 | |
| - binutils_linux-64=2.31.1=h6176602_6 | |
| - biopython=1.71=py27h637b7d7_0 | |
| - bitarray=0.8.3=py27h14c3975_0 | |
| - bkcharts=0.2=py27h241ae91_0 | |
| - blas=1.0=mkl | |
| - blaze=0.11.3=py27_0 | |
| - bleach=3.0.2=py27_0 | |
| - blosc=1.14.4=hdbcaa40_0 | |
| - bokeh=1.0.2=py27_0 | |
| - boto=2.49.0=py27_0 | |
| - bottleneck=1.2.1=py27h21b16a3_0 | |
| - bwidget=1.9.11=1 | |
| - bx-python=0.7.3=py27_0 | |
| - bzip2=1.0.6=h14c3975_5 | |
| - ca-certificates=2019.1.23=0 | |
| - cairo=1.14.12=h8948797_3 | |
| - cdecimal=2.3=py27h14c3975_3 | |
| - cdna_cupcake=5.8=py27_0 | |
| - certifi=2019.3.9=py27_0 | |
| - cffi=1.11.5=py27he75722e_1 | |
| - chardet=3.0.4=py27_1 | |
| - click=7.0=py27_0 | |
| - cloudpickle=0.6.1=py27_0 | |
| - clyent=1.2.2=py27_1 | |
| - colorama=0.4.1=py27_0 | |
| - configparser=3.5.0=py27h5117587_0 | |
| - contextlib2=0.5.5=py27hbf4c468_0 | |
| - cryptography=2.4.2=py27h1ba5d50_0 | |
| - curl=7.63.0=hbc83047_1000 | |
| - cycler=0.10.0=py27hc7354d3_0 | |
| - cython=0.29.2=py27he6710b0_0 | |
| - cytoolz=0.9.0.1=py27h14c3975_1 | |
| - dask=0.15.2=py27_0 | |
| - dask-core=1.0.0=py27_0 | |
| - datashape=0.5.4=py27_1 | |
| - dbus=1.13.2=h714fa37_1 | |
| - decorator=4.3.0=py27_0 | |
| - defusedxml=0.5.0=py27_1 | |
| - distributed=1.25.1=py27_0 | |
| - docutils=0.14=py27hae222c1_0 | |
| - entrypoints=0.2.3=py27_2 | |
| - enum34=1.1.6=py27_1 | |
| - et_xmlfile=1.0.1=py27h75840f5_0 | |
| - expat=2.2.6=he6710b0_0 | |
| - fastcache=1.0.2=py27h14c3975_2 | |
| - filelock=3.0.10=py27_0 | |
| - flask=1.0.2=py27_1 | |
| - flask-cors=3.0.7=py27_0 | |
| - fontconfig=2.13.0=h9420a91_0 | |
| - freetype=2.9.1=h8a8886c_1 | |
| - fribidi=1.0.5=h7b6447c_0 | |
| - funcsigs=1.0.2=py27h83f16ab_0 | |
| - functools32=3.2.3.2=py27_1 | |
| - future=0.17.1=py27_0 | |
| - futures=3.2.0=py27_0 | |
| - gcc_impl_linux-64=7.3.0=habb00fd_1 | |
| - gcc_linux-64=7.3.0=h553295d_6 | |
| - get_terminal_size=1.0.0=haa9412d_0 | |
| - gevent=1.3.7=py27h7b6447c_1 | |
| - gffread=0.9.12=0 | |
| - gfortran_impl_linux-64=7.3.0=hdf63c60_1 | |
| - gfortran_linux-64=7.3.0=h553295d_6 | |
| - glib=2.56.2=hd408876_0 | |
| - glob2=0.6=py27_1 | |
| - gmp=6.1.2=h6c8ec71_1 | |
| - gmpy2=2.0.8=py27h10f8cd9_2 | |
| - graphite2=1.3.12=h23475e2_2 | |
| - graphviz=2.40.1=h21bd128_2 | |
| - greenlet=0.4.15=py27h7b6447c_0 | |
| - grin=1.2.1=py27_4 | |
| - gsl=2.4=h14c3975_4 | |
| - gst-plugins-base=1.14.0=hbbd80ab_1 | |
| - gstreamer=1.14.0=hb453b48_1 | |
| - gxx_impl_linux-64=7.3.0=hdf63c60_1 | |
| - gxx_linux-64=7.3.0=h553295d_6 | |
| - h5py=2.8.0=py27h8d01980_0 | |
| - harfbuzz=1.8.8=hffaf4a1_0 | |
| - hdf5=1.10.2=hba1933b_1 | |
| - heapdict=1.0.0=py27_2 | |
| - html5lib=1.0.1=py27_0 | |
| - htslib=1.9=h47928c2_5 | |
| - icu=58.2=h9c2bf20_1 | |
| - idna=2.8=py27_0 | |
| - imageio=2.4.1=py27_0 | |
| - imagesize=1.1.0=py27_0 | |
| - importlib_metadata=0.6=py27_0 | |
| - intel-openmp=2019.1=144 | |
| - ipaddress=1.0.22=py27_0 | |
| - ipykernel=4.10.0=py27_0 | |
| - ipython=5.8.0=py27_0 | |
| - ipython_genutils=0.2.0=py27h89fb69b_0 | |
| - ipywidgets=7.4.2=py27_0 | |
| - iso8601=0.1.12=py27_1 | |
| - isort=4.3.4=py27_0 | |
| - isoseq3=3.1.0=0 | |
| - itsdangerous=1.1.0=py27_0 | |
| - jbig=2.1=hdba287a_0 | |
| - jdcal=1.4=py27_0 | |
| - jedi=0.13.2=py27_0 | |
| - jinja2=2.10=py27_0 | |
| - jpeg=9b=h024ee3a_2 | |
| - jsonschema=2.6.0=py27h7ed5aa4_0 | |
| - jupyter=1.0.0=py27_7 | |
| - jupyter_client=5.2.4=py27_0 | |
| - jupyter_console=5.2.0=py27_1 | |
| - jupyter_core=4.4.0=py27_0 | |
| - jupyterlab=0.33.11=py27_0 | |
| - jupyterlab_launcher=0.11.2=py27h28b3542_0 | |
| - kiwisolver=1.0.1=py27hf484d3e_0 | |
| - krb5=1.16.1=h173b8e3_7 | |
| - lazy-object-proxy=1.3.1=py27h14c3975_2 | |
| - libarchive=3.3.3=h5d8350f_5 | |
| - libcurl=7.63.0=h20c2e04_1000 | |
| - libdeflate=1.0=h14c3975_1 | |
| - libedit=3.1.20170329=h6b74fdf_2 | |
| - libffi=3.2.1=hd88cf55_4 | |
| - libgcc-ng=8.2.0=hdf63c60_1 | |
| - libgfortran-ng=7.3.0=hdf63c60_0 | |
| - liblief=0.9.0=h7725739_1 | |
| - libpng=1.6.35=hbc83047_0 | |
| - libsodium=1.0.16=h1bed415_0 | |
| - libssh2=1.8.0=h1ba5d50_4 | |
| - libstdcxx-ng=8.2.0=hdf63c60_1 | |
| - libtiff=4.0.9=he85c1e1_2 | |
| - libtool=2.4.6=h7b6447c_5 | |
| - libuuid=1.0.3=h1bed415_2 | |
| - libxcb=1.13=h1bed415_1 | |
| - libxml2=2.9.8=h26e45fe_1 | |
| - libxslt=1.1.32=h1312cb7_0 | |
| - lima=1.8.0=0 | |
| - linecache2=1.0.0=py27_0 | |
| - llvm=3.3=0 | |
| - llvmlite=0.26.0=py27hd408876_0 | |
| - llvmpy=0.12.7=py27_0 | |
| - locket=0.2.0=py27h73929a2_1 | |
| - lxml=4.2.5=py27hefd8a0e_0 | |
| - lz4-c=1.8.1.2=h14c3975_0 | |
| - lzo=2.10=h49e0be7_2 | |
| - make=4.2.1=h1bed415_1 | |
| - markupsafe=1.1.0=py27h7b6447c_0 | |
| - matplotlib=2.2.3=py27hb69df0a_0 | |
| - mccabe=0.6.1=py27_1 | |
| - minimap2=2.16=h84994c4_1 | |
| - mistune=0.8.4=py27h7b6447c_0 | |
| - mkl=2019.1=144 | |
| - mkl-service=1.1.2=py27he904b0f_5 | |
| - mkl_fft=1.0.6=py27hd81dba3_0 | |
| - mkl_random=1.0.2=py27hd81dba3_0 | |
| - more-itertools=4.3.0=py27_0 | |
| - mpc=1.1.0=h10f8cd9_1 | |
| - mpfr=4.0.1=hdf1c602_3 | |
| - mpmath=1.1.0=py27_0 | |
| - msgpack-python=0.5.6=py27h6bb024c_1 | |
| - multipledispatch=0.6.0=py27_0 | |
| - nbconvert=5.4.0=py27_1 | |
| - nbformat=4.4.0=py27hed7f2b2_0 | |
| - ncurses=6.1=he6710b0_1 | |
| - networkx=2.2=py27_1 | |
| - nltk=3.4=py27_1 | |
| - nose=1.3.7=py27_2 | |
| - notebook=5.7.4=py27_0 | |
| - numba=0.41.0=py27h962f231_0 | |
| - numexpr=2.6.9=py27h9e4a6bb_0 | |
| - numpy=1.15.4=py27h7e9f1db_0 | |
| - numpy-base=1.15.4=py27hde5b4d6_0 | |
| - numpydoc=0.8.0=py27_0 | |
| - odo=0.5.1=py27h9170de3_0 | |
| - olefile=0.46=py27_0 | |
| - openpyxl=2.5.12=py27_0 | |
| - openssl=1.1.1b=h7b6447c_1 | |
| - packaging=18.0=py27_0 | |
| - pandas=0.23.1=py27h637b7d7_0 | |
| - pandoc=1.19.2.1=hea2e7c5_1 | |
| - pandocfilters=1.4.2=py27_1 | |
| - pango=1.42.4=h049681c_0 | |
| - parso=0.3.1=py27_0 | |
| - partd=0.3.9=py27_0 | |
| - patchelf=0.9=he6710b0_3 | |
| - path.py=11.5.0=py27_0 | |
| - pathlib2=2.3.3=py27_0 | |
| - patsy=0.5.1=py27_0 | |
| - pbccs=3.4.0=0 | |
| - pbcommand=1.1.1=py27h24bf2e0_1 | |
| - pbcore=1.5.1=py27_1 | |
| - pbcoretools=0.2.4=py27_1 | |
| - pcre=8.42=h439df22_0 | |
| - pep8=1.7.1=py27_0 | |
| - pexpect=4.6.0=py27_0 | |
| - pickleshare=0.7.5=py27_0 | |
| - pigz=2.4=h84994c4_0 | |
| - pillow=5.3.0=py27h34e0f95_0 | |
| - pip=18.1=py27_0 | |
| - pixman=0.34.0=hceecf20_3 | |
| - pkginfo=1.4.2=py27_1 | |
| - pluggy=0.8.0=py27_0 | |
| - ply=3.11=py27_0 | |
| - prometheus_client=0.5.0=py27_0 | |
| - prompt_toolkit=1.0.15=py27h1b593e1_0 | |
| - psutil=5.4.8=py27h7b6447c_0 | |
| - ptyprocess=0.6.0=py27_0 | |
| - py=1.7.0=py27_0 | |
| - py-lief=0.9.0=py27h7725739_1 | |
| - pycairo=1.18.0=py27h2a1e443_0 | |
| - pycodestyle=2.4.0=py27_0 | |
| - pycosat=0.6.3=py27h14c3975_0 | |
| - pycparser=2.19=py27_0 | |
| - pycrypto=2.6.1=py27h14c3975_9 | |
| - pycurl=7.43.0.2=py27h1ba5d50_0 | |
| - pyflakes=2.0.0=py27_0 | |
| - pygments=2.3.1=py27_0 | |
| - pylint=1.9.2=py27_0 | |
| - pyodbc=4.0.25=py27he6710b0_0 | |
| - pyopenssl=18.0.0=py27_0 | |
| - pyparsing=2.3.0=py27_0 | |
| - pyqt=5.9.2=py27h05f1152_2 | |
| - pysam=0.15.2=py27h1671916_1 | |
| - pysocks=1.6.8=py27_0 | |
| - pytables=3.4.4=py27h02b9ad4_0 | |
| - pytest=4.0.2=py27_0 | |
| - python=2.7.15=h9bab390_6 | |
| - python-dateutil=2.7.5=py27_0 | |
| - python-libarchive-c=2.8=py27_6 | |
| - pytz=2018.7=py27_0 | |
| - pywavelets=0.5.2=py27hecda097_0 | |
| - pyyaml=3.13=py27h14c3975_0 | |
| - pyzmq=17.1.2=py27h14c3975_0 | |
| - qt=5.9.7=h5867ecd_1 | |
| - qtawesome=0.5.3=py27_0 | |
| - qtconsole=4.4.3=py27_0 | |
| - qtpy=1.5.2=py27_0 | |
| - r-base=3.5.1=h1e0a451_2 | |
| - readline=7.0=h7b6447c_5 | |
| - requests=2.21.0=py27_0 | |
| - rope=0.11.0=py27_0 | |
| - ruamel_yaml=0.15.46=py27h14c3975_0 | |
| - samtools=1.9=h91753b0_5 | |
| - scandir=1.9.0=py27h14c3975_0 | |
| - scikit-image=0.14.2=py27he6710b0_0 | |
| - scikit-learn=0.20.3=py27hd81dba3_0 | |
| - scipy=1.2.1=py27h7c811a0_0 | |
| - seaborn=0.9.0=py27_0 | |
| - send2trash=1.5.0=py27_0 | |
| - seqkit=0.10.1=1 | |
| - setuptools=40.6.3=py27_0 | |
| - simplegeneric=0.8.1=py27_2 | |
| - singledispatch=3.4.0.3=py27h9bcb476_0 | |
| - sip=4.19.8=py27hf484d3e_0 | |
| - six=1.12.0=py27_0 | |
| - snappy=1.1.7=hbae5bb6_3 | |
| - snowballstemmer=1.2.1=py27h44e2768_0 | |
| - sortedcollections=1.0.1=py27_0 | |
| - sortedcontainers=2.1.0=py27_0 | |
| - sphinx=1.8.2=py27_0 | |
| - sphinxcontrib=1.0=py27_1 | |
| - sphinxcontrib-websupport=1.1.0=py27_1 | |
| - spyder=3.3.2=py27_0 | |
| - spyder-kernels=0.3.0=py27_0 | |
| - sqlalchemy=1.2.15=py27h7b6447c_0 | |
| - sqlite=3.26.0=h7b6447c_0 | |
| - ssl_match_hostname=3.5.0.1=py27_2 | |
| - statsmodels=0.9.0=py27h3010b51_0 | |
| - subprocess32=3.5.3=py27h7b6447c_0 | |
| - sympy=1.3=py27_0 | |
| - system=5.8=2 | |
| - tblib=1.3.2=py27h51fe5ba_0 | |
| - terminado=0.8.1=py27_1 | |
| - testpath=0.4.2=py27_0 | |
| - tk=8.6.8=hbc83047_0 | |
| - tktable=2.10=h14c3975_0 | |
| - toolz=0.9.0=py27_0 | |
| - tornado=5.1.1=py27h7b6447c_0 | |
| - tqdm=4.28.1=py27h28b3542_0 | |
| - traceback2=1.4.0=py27_0 | |
| - traitlets=4.3.2=py27hd6ce930_0 | |
| - typing=3.6.6=py27_0 | |
| - unicodecsv=0.14.1=py27h5062da9_0 | |
| - unittest2=1.1.0=py27_0 | |
| - unixodbc=2.3.7=h14c3975_0 | |
| - urllib3=1.24.1=py27_0 | |
| - wcwidth=0.1.7=py27h9e3e1ab_0 | |
| - webencodings=0.5.1=py27_1 | |
| - werkzeug=0.14.1=py27_0 | |
| - wheel=0.32.3=py27_0 | |
| - widgetsnbextension=3.4.2=py27_0 | |
| - wrapt=1.10.11=py27h14c3975_2 | |
| - wurlitzer=1.0.2=py27_0 | |
| - xlrd=1.2.0=py27_0 | |
| - xlsxwriter=1.1.2=py27_0 | |
| - xlwt=1.3.0=py27h3d85d97_0 | |
| - xz=5.2.4=h14c3975_4 | |
| - yaml=0.1.7=had09818_2 | |
| - zeromq=4.2.5=hf484d3e_1 | |
| - zict=0.1.3=py27_0 | |
| - zlib=1.2.11=h7b6447c_3 | |
| - zstd=1.3.7=h0b5b093_0 | |
| - pip: | |
| - cupcake==6.7 | |
| prefix: /home/HIC/.conda/envs/anaCogent5.2 |
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