Commit #1 - Pushing Snakemake Pipeline, References, and Jupyter noteb…

…ooks

CondaEnvs/IlluminaPE_Processing_Conda.yml

@@ -0,0 +1,72 @@
+name: IlluminaPE_Processing
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+  - r
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - alsa-lib=1.1.5=h516909a_1001
+  - bwa=0.7.17=hed695b0_6
+  - bzip2=1.0.8=h516909a_1
+  - ca-certificates=2019.9.11=hecc5488_0
+  - certifi=2019.9.11=py38_0
+  - curl=7.65.3=hf8cf82a_0
+  - fontconfig=2.13.1=h86ecdb6_1001
+  - freetype=2.10.0=he983fc9_1
+  - giflib=5.1.7=h516909a_1
+  - htslib=1.9=h4da6232_3
+  - icu=64.2=he1b5a44_1
+  - jpeg=9c=h14c3975_1001
+  - krb5=1.16.3=h05b26f9_1001
+  - lcms2=2.9=hbd6801e_1
+  - ld_impl_linux-64=2.33.1=h53a641e_7
+  - libcurl=7.65.3=hda55be3_0
+  - libdeflate=1.2=h516909a_1
+  - libedit=3.1.20170329=hf8c457e_1001
+  - libffi=3.2.1=he1b5a44_1006
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libiconv=1.15=h516909a_1005
+  - libpng=1.6.37=hed695b0_0
+  - libssh2=1.8.2=h22169c7_2
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - libtiff=4.1.0=hc3755c2_1
+  - libuuid=2.32.1=h14c3975_1000
+  - libxcb=1.13=h14c3975_1002
+  - libxml2=2.9.10=hee79883_0
+  - lz4-c=1.8.3=he1b5a44_1001
+  - ncurses=6.1=hf484d3e_1002
+  - openjdk=11.0.1=h46a85a0_1017
+  - openssl=1.1.1d=h516909a_0
+  - perl=5.26.2=h516909a_1006
+  - picard-slim=2.21.4=0
+  - pilon=1.23=2
+  - pip=19.3.1=py38_0
+  - pthread-stubs=0.4=h14c3975_1001
+  - python=3.8.0=h357f687_5
+  - readline=8.0=hf8c457e_0
+  - samtools=1.9=h10a08f8_12
+  - setuptools=42.0.1=py38_0
+  - sqlite=3.30.1=hcee41ef_0
+  - tk=8.6.10=hed695b0_0
+  - wheel=0.33.6=py38_0
+  - xorg-fixesproto=5.0=h14c3975_1002
+  - xorg-inputproto=2.3.2=h14c3975_1002
+  - xorg-kbproto=1.0.7=h14c3975_1002
+  - xorg-libx11=1.6.9=h516909a_0
+  - xorg-libxau=1.0.9=h14c3975_0
+  - xorg-libxdmcp=1.1.3=h516909a_0
+  - xorg-libxext=1.3.4=h516909a_0
+  - xorg-libxfixes=5.0.3=h516909a_1004
+  - xorg-libxi=1.7.10=h516909a_0
+  - xorg-libxrender=0.9.10=h516909a_1002
+  - xorg-libxtst=1.2.3=h516909a_1002
+  - xorg-recordproto=1.14.2=h516909a_1002
+  - 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_1006
+  - zstd=1.4.4=h3b9ef0a_1
+prefix: /home/mgmarin/anaconda3/envs/IlluminaPE_Processing
+

CondaEnvs/PacBio_Software_py27_Conda.yml

@@ -0,0 +1,80 @@
+name: PacBio_Software_py27
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+  - r
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - avro-python2=1.9.0=py_0
+  - bam2fastx=1.3.0=he1c1bb9_8
+  - bax2bam=0.0.9=h018d624_7
+  - blasr=5.3.2=h4ef8376_2
+  - blasr_libcpp=5.3.3=h018d624_1
+  - boost=1.67.0=py27h3e44d54_0
+  - boost-cpp=1.67.0=h3a22d5f_0
+  - bzip2=1.0.8=h516909a_1
+  - ca-certificates=2019.9.11=hecc5488_0
+  - certifi=2019.9.11=py27_0
+  - cffi=1.13.2=py27h8022711_0
+  - chardet=3.0.4=py27_1003
+  - cryptography=2.8=py27h72c5cf5_0
+  - curl=7.65.3=hf8cf82a_0
+  - cython=0.29.14=py27he1b5a44_0
+  - enum34=1.1.6=py27_1002
+  - flye=2.6=py27he513fc3_0
+  - genomicconsensus=2.3.3=py_1
+  - h5py=2.10.0=nompi_py27h513d04c_100
+  - hdf5=1.10.5=nompi_h3c11f04_1104
+  - htslib=1.9=ha228f0b_7
+  - icu=58.2=hf484d3e_1000
+  - idna=2.8=py27_1000
+  - ipaddress=1.0.23=py_0
+  - iso8601=0.1.12=py_1
+  - krb5=1.16.3=h05b26f9_1001
+  - libblas=3.8.0=14_openblas
+  - libcblas=3.8.0=14_openblas
+  - libcurl=7.65.3=hda55be3_0
+  - libdeflate=1.0=h14c3975_1
+  - libedit=3.1.20170329=hf8c457e_1001
+  - libffi=3.2.1=he1b5a44_1006
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libgfortran-ng=7.3.0=hdf63c60_2
+  - liblapack=3.8.0=14_openblas
+  - libopenblas=0.3.7=h6e990d7_3
+  - libssh2=1.8.2=h22169c7_2
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - linecache2=1.0.0=py_1
+  - minimap2=2.17=h8b12597_1
+  - ncurses=6.1=hf484d3e_1002
+  - numpy=1.16.5=py27h95a1406_0
+  - openssl=1.1.1d=h516909a_0
+  - pbbam=1.0.6=hc16d5b3_1
+  - pbcommand=1.1.1=py_3
+  - pbcopper=1.3.0=h3e4de3e_0
+  - pbcore=1.7.1=py27_0
+  - pbmm2=1.1.0=hfb76ee0_0
+  - pip=19.3.1=py27_0
+  - pycparser=2.19=py27_1
+  - pyopenssl=19.0.0=py27_0
+  - pysam=0.15.3=py27hda2845c_1
+  - pysocks=1.7.1=py27_0
+  - python=2.7.15=h5a48372_1009
+  - python-consensuscore=1.1.1=py27h3f2a3d2_3
+  - python-consensuscore2=3.4.1=py27_0
+  - pytz=2019.3=py_0
+  - readline=8.0=hf8c457e_0
+  - requests=2.22.0=py27_1
+  - samtools=1.9=h10a08f8_12
+  - setuptools=41.6.0=py27_1
+  - six=1.13.0=py27_0
+  - sqlite=3.30.1=hcee41ef_0
+  - tk=8.6.9=hed695b0_1003
+  - traceback2=1.4.0=py27_0
+  - unittest2=1.1.0=py_0
+  - urllib3=1.25.7=py27_0
+  - wheel=0.33.6=py27_0
+  - xz=5.2.4=h14c3975_1001
+  - zlib=1.2.11=h516909a_1006
+prefix: /home/mgmarin/anaconda3/envs/PacBio_Software_py27
+