kelly-sovacool/README.md

## README.md

      
    Raw
  

              README.md
            
          
    test-conda-env-hpc

Question

Does the conda environment that you have activated on the login node also get used in the compute nodes when submitting a job?
Methods


Used conda version 4.6.14


Activate a conda env with snakemake installed.

Submit the job & note the job id.
The log file should have snakemake output.


Activate a conda env without snakemake.

Submit the job & note the job id.
The log file should have an error message that the snakemake command was not found.


SLURM


HPC: beta-login.stage.arc-ts.umich.edu
Script: submit-slurm.sh
Conda environments:

With snakemake: slurm-with-smk.yaml
Without snakemake: slurm-no-smk.yaml


PBS-Torque


HPC: flux-login.arc-ts.umich.edu
Script: submit-pbs.sh
Conda environments:

With snakemake: pbs-with-smk.yaml
Without snakemake: pbs-no-smk.yaml


Results

SLURM job with snakemake: 33069

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
		1	touch
		1

[Mon Jun  3 14:06:20 2019]
rule touch:
	output: file.txt
	jobid: 0

[Mon Jun  3 14:06:20 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env/.snakemake/log/2019-06-03T140620.029171.snakemake.log

SLURM job without snakemake: 33070

Conda environment: slurm-no-smk.yaml
/var/spool/slurmd.spool/job33070/slurm_script: line 49: snakemake: command not found

PBS job with snakemake: 33732423

nyx5568
/home/sovacool/test-conda-env-hpc
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	touch
	1

[Wed Jun  5 11:01:27 2019]
rule touch:
    output: file.txt
    jobid: 0

[Wed Jun  5 11:01:27 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env-hpc/.snakemake/log/2019-06-05T110127.477703.snakemake.log

PBS job without snakemake: 33732416

nyx5089
/home/sovacool/test-conda-env-hpc
/var/spool/torque/mom_priv/jobs/33732416.nyx.arc-ts.umich.edu.SC: line 21: snakemake: command not found

Conclusion

Yes!

  
## pbs-no-smk.yaml
name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _ipyw_jlab_nb_ext_conf=0.1.0=py37_0
  - alabaster=0.7.11=py37_0
  - anaconda=custom=py37_0
  - anaconda-client=1.7.2=py37_0
  - anaconda-navigator=1.9.2=py37_0
  - anaconda-project=0.8.2=py37_0
  - appdirs=1.4.3=py37h28b3542_0
  - asn1crypto=0.24.0=py37_0
  - astroid=2.0.4=py37_0
  - astropy=3.0.4=py37h14c3975_0
  - atomicwrites=1.2.1=py37_0
  - attrs=18.2.0=py37h28b3542_0
  - automat=0.7.0=py37_0
  - babel=2.6.0=py37_0
  - backcall=0.1.0=py37_0
  - backports=1.0=py37_1
  - backports.shutil_get_terminal_size=1.0.0=py37_2
  - beautifulsoup4=4.6.3=py37_0
  - bitarray=0.8.3=py37h14c3975_0
  - bkcharts=0.2=py37_0
  - blas=1.0=mkl
  - blaze=0.11.3=py37_0
  - bleach=2.1.4=py37_0
  - blosc=1.14.4=hdbcaa40_0
  - bokeh=0.13.0=py37_0
  - boto=2.49.0=py37_0
  - bottleneck=1.2.1=py37h035aef0_1
  - bzip2=1.0.6=h14c3975_5
  - ca-certificates=2019.5.15=0
  - cairo=1.14.12=h8948797_3
  - certifi=2019.3.9=py37_0
  - cffi=1.11.5=py37he75722e_1
  - chardet=3.0.4=py37_1
  - click=6.7=py37_0
  - cloudpickle=0.5.5=py37_0
  - clyent=1.2.2=py37_1
  - colorama=0.3.9=py37_0
  - conda=4.6.14=py37_0
  - conda-build=3.15.1=py37_0
  - conda-env=2.6.0=1
  - constantly=15.1.0=py37h28b3542_0
  - contextlib2=0.5.5=py37_0
  - cryptography=2.6.1=py37h1ba5d50_0
  - curl=7.64.1=hbc83047_0
  - cycler=0.10.0=py37_0
  - cython=0.28.5=py37hf484d3e_0
  - cytoolz=0.9.0.1=py37h14c3975_1
  - dask=0.19.1=py37_0
  - dask-core=0.19.1=py37_0
  - datashape=0.5.4=py37_1
  - dbus=1.13.2=h714fa37_1
  - decorator=4.3.0=py37_0
  - defusedxml=0.5.0=py37_1
  - distributed=1.23.1=py37_0
  - docutils=0.14=py37_0
  - entrypoints=0.2.3=py37_2
  - et_xmlfile=1.0.1=py37_0
  - expat=2.2.6=he6710b0_0
  - fastcache=1.0.2=py37h14c3975_2
  - filelock=3.0.8=py37_0
  - flask=1.0.2=py37_1
  - flask-cors=3.0.6=py37_0
  - fontconfig=2.13.0=h9420a91_0
  - freetype=2.9.1=h8a8886c_1
  - fribidi=1.0.5=h7b6447c_0
  - get_terminal_size=1.0.0=haa9412d_0
  - gevent=1.3.6=py37h7b6447c_0
  - glib=2.56.2=hd408876_0
  - glob2=0.6=py37_0
  - gmp=6.1.2=h6c8ec71_1
  - gmpy2=2.0.8=py37h10f8cd9_2
  - graphite2=1.3.12=h23475e2_2
  - greenlet=0.4.15=py37h7b6447c_0
  - gst-plugins-base=1.14.0=hbbd80ab_1
  - gstreamer=1.14.0=hb453b48_1
  - h5py=2.8.0=py37h989c5e5_3
  - harfbuzz=1.8.8=hffaf4a1_0
  - hdf5=1.10.2=hba1933b_1
  - heapdict=1.0.0=py37_2
  - html5lib=1.0.1=py37_0
  - hyperlink=18.0.0=py37_0
  - icu=58.2=h9c2bf20_1
  - idna=2.7=py37_0
  - imageio=2.4.1=py37_0
  - imagesize=1.1.0=py37_0
  - incremental=17.5.0=py37_0
  - intel-openmp=2019.0=118
  - ipykernel=4.9.0=py37_1
  - ipython=6.5.0=py37_0
  - ipython_genutils=0.2.0=py37_0
  - ipywidgets=7.4.1=py37_0
  - isort=4.3.4=py37_0
  - itsdangerous=0.24=py37_1
  - jbig=2.1=hdba287a_0
  - jdcal=1.4=py37_0
  - jedi=0.12.1=py37_0
  - jeepney=0.3.1=py37_0
  - jinja2=2.10=py37_0
  - jpeg=9b=h024ee3a_2
  - jsonschema=2.6.0=py37_0
  - jupyter=1.0.0=py37_7
  - jupyter_client=5.2.3=py37_0
  - jupyter_console=5.2.0=py37_1
  - jupyter_core=4.4.0=py37_0
  - jupyterlab=0.34.9=py37_0
  - jupyterlab_launcher=0.13.1=py37_0
  - keyring=13.2.1=py37_0
  - kiwisolver=1.0.1=py37hf484d3e_0
  - krb5=1.16.1=h173b8e3_7
  - lazy-object-proxy=1.3.1=py37h14c3975_2
  - libcurl=7.64.1=h20c2e04_0
  - 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
  - libpng=1.6.37=hbc83047_0
  - libsodium=1.0.16=h1bed415_0
  - libssh2=1.8.2=h1ba5d50_0
  - libstdcxx-ng=8.2.0=hdf63c60_1
  - libtiff=4.0.9=he85c1e1_2
  - libtool=2.4.6=h544aabb_3
  - libuuid=1.0.3=h1bed415_2
  - libxcb=1.13=h1bed415_1
  - libxml2=2.9.8=h26e45fe_1
  - libxslt=1.1.32=h1312cb7_0
  - llvmlite=0.24.0=py37hdbcaa40_0
  - locket=0.2.0=py37_1
  - lxml=4.2.5=py37hefd8a0e_0
  - lzo=2.10=h49e0be7_2
  - markupsafe=1.0=py37h14c3975_1
  - matplotlib=2.2.3=py37hb69df0a_0
  - mccabe=0.6.1=py37_1
  - mistune=0.8.3=py37h14c3975_1
  - mkl=2019.0=118
  - mkl-service=1.1.2=py37h90e4bf4_5
  - mkl_fft=1.0.4=py37h4414c95_1
  - mkl_random=1.0.1=py37h4414c95_1
  - more-itertools=4.3.0=py37_0
  - mpc=1.1.0=h10f8cd9_1
  - mpfr=4.0.1=hdf1c602_3
  - mpmath=1.0.0=py37_2
  - msgpack-python=0.5.6=py37h6bb024c_1
  - multipledispatch=0.6.0=py37_0
  - navigator-updater=0.2.1=py37_0
  - nbconvert=5.4.0=py37_1
  - nbformat=4.4.0=py37_0
  - ncurses=6.1=hf484d3e_0
  - networkx=2.1=py37_0
  - nltk=3.3.0=py37_0
  - nose=1.3.7=py37_2
  - notebook=5.6.0=py37_0
  - numba=0.39.0=py37h04863e7_0
  - numexpr=2.6.8=py37hd89afb7_0
  - numpy=1.15.1=py37h1d66e8a_0
  - numpy-base=1.15.1=py37h81de0dd_0
  - numpydoc=0.8.0=py37_0
  - odo=0.5.1=py37_0
  - olefile=0.46=py37_0
  - openpyxl=2.5.6=py37_0
  - openssl=1.1.1c=h7b6447c_1
  - packaging=17.1=py37_0
  - pandas=0.23.4=py37h04863e7_0
  - pandoc=1.19.2.1=hea2e7c5_1
  - pandocfilters=1.4.2=py37_1
  - pango=1.42.4=h049681c_0
  - parso=0.3.1=py37_0
  - partd=0.3.8=py37_0
  - patchelf=0.9=hf484d3e_2
  - path.py=11.1.0=py37_0
  - pathlib2=2.3.2=py37_0
  - patsy=0.5.0=py37_0
  - pcre=8.42=h439df22_0
  - pep8=1.7.1=py37_0
  - pexpect=4.6.0=py37_0
  - pickleshare=0.7.4=py37_0
  - pillow=5.2.0=py37heded4f4_0
  - pip=10.0.1=py37_0
  - pixman=0.34.0=hceecf20_3
  - pkginfo=1.4.2=py37_1
  - pluggy=0.7.1=py37h28b3542_0
  - ply=3.11=py37_0
  - prometheus_client=0.3.1=py37h28b3542_0
  - prompt_toolkit=1.0.15=py37_0
  - psutil=5.4.7=py37h14c3975_0
  - ptyprocess=0.6.0=py37_0
  - py=1.6.0=py37_0
  - pyasn1=0.4.4=py37h28b3542_0
  - pyasn1-modules=0.2.2=py37_0
  - pycodestyle=2.4.0=py37_0
  - pycosat=0.6.3=py37h14c3975_0
  - pycparser=2.18=py37_1
  - pycrypto=2.6.1=py37h14c3975_9
  - pycurl=7.43.0.2=py37h1ba5d50_0
  - pyflakes=2.0.0=py37_0
  - pygments=2.2.0=py37_0
  - pylint=2.1.1=py37_0
  - pyodbc=4.0.24=py37he6710b0_0
  - pyopenssl=18.0.0=py37_0
  - pyparsing=2.2.0=py37_1
  - pyqt=5.9.2=py37h05f1152_2
  - pysocks=1.6.8=py37_0
  - pytables=3.4.4=py37ha205bf6_0
  - pytest=3.8.0=py37_0
  - pytest-arraydiff=0.2=py37h39e3cac_0
  - pytest-astropy=0.4.0=py37_0
  - pytest-doctestplus=0.1.3=py37_0
  - pytest-openfiles=0.3.0=py37_0
  - pytest-remotedata=0.3.0=py37_0
  - python=3.7.2=h0371630_0
  - python-dateutil=2.7.3=py37_0
  - pytz=2018.5=py37_0
  - pywavelets=1.0.0=py37hdd07704_0
  - pyyaml=3.13=py37h14c3975_0
  - pyzmq=17.1.2=py37h14c3975_0
  - qt=5.9.7=h5867ecd_1
  - qtawesome=0.4.4=py37_0
  - qtconsole=4.4.1=py37_0
  - qtpy=1.5.0=py37_0
  - readline=7.0=h7b6447c_5
  - requests=2.19.1=py37_0
  - rope=0.11.0=py37_0
  - ruamel_yaml=0.15.46=py37h14c3975_0
  - scikit-image=0.14.0=py37hf484d3e_1
  - scikit-learn=0.19.2=py37h4989274_0
  - scipy=1.1.0=py37hfa4b5c9_1
  - seaborn=0.9.0=py37_0
  - secretstorage=3.1.0=py37_0
  - send2trash=1.5.0=py37_0
  - service_identity=17.0.0=py37h28b3542_0
  - setuptools=40.2.0=py37_0
  - simplegeneric=0.8.1=py37_2
  - singledispatch=3.4.0.3=py37_0
  - sip=4.19.8=py37hf484d3e_0
  - six=1.11.0=py37_1
  - snappy=1.1.7=hbae5bb6_3
  - snowballstemmer=1.2.1=py37_0
  - sortedcollections=1.0.1=py37_0
  - sortedcontainers=2.0.5=py37_0
  - sphinx=1.7.9=py37_0
  - sphinxcontrib=1.0=py37_1
  - sphinxcontrib-websupport=1.1.0=py37_1
  - spyder=3.3.1=py37_1
  - spyder-kernels=0.2.6=py37_0
  - sqlalchemy=1.2.11=py37h7b6447c_0
  - sqlite=3.26.0=h7b6447c_0
  - statsmodels=0.9.0=py37h035aef0_0
  - sympy=1.2=py37_0
  - tblib=1.3.2=py37_0
  - terminado=0.8.1=py37_1
  - testpath=0.3.1=py37_0
  - tk=8.6.8=hbc83047_0
  - toolz=0.9.0=py37_0
  - tornado=5.1=py37h14c3975_0
  - tqdm=4.26.0=py37h28b3542_0
  - traitlets=4.3.2=py37_0
  - twisted=18.7.0=py37h14c3975_1
  - unicodecsv=0.14.1=py37_0
  - unixodbc=2.3.7=h14c3975_0
  - urllib3=1.23=py37_0
  - wcwidth=0.1.7=py37_0
  - webencodings=0.5.1=py37_1
  - werkzeug=0.14.1=py37_0
  - wheel=0.31.1=py37_0
  - widgetsnbextension=3.4.1=py37_0
  - wrapt=1.10.11=py37h14c3975_2
  - xlrd=1.1.0=py37_1
  - xlsxwriter=1.1.0=py37_0
  - xlwt=1.3.0=py37_0
  - xz=5.2.4=h14c3975_4
  - yaml=0.1.7=had09818_2
  - zeromq=4.2.5=hf484d3e_1
  - zict=0.1.3=py37_0
  - zlib=1.2.11=ha838bed_2
  - zope=1.0=py37_1
  - zope.interface=4.5.0=py37h14c3975_0
  - pip:
    - arrow==0.12.1
    - binaryornot==0.4.4
    - cookiecutter==1.6.0
    - future==0.17.1
    - jinja2-time==0.2.0
    - poyo==0.4.2
    - whichcraft==0.5.2
prefix: /home/sovacool/bin/anaconda3


## pbs-with-smk.yaml
name: optiFit
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _r-mutex=1.0.0=anacondar_1
  - aioeasywebdav=2.2.0=py36_0
  - aiohttp=3.5.4=py36h14c3975_0
  - appdirs=1.4.3=py_1
  - asn1crypto=0.24.0=py36_1003
  - async-timeout=3.0.1=py_1000
  - attrs=19.1.0=py_0
  - bcrypt=3.1.4=py36h470a237_0
  - binutils_impl_linux-64=2.31.1=h6176602_1
  - binutils_linux-64=2.31.1=h6176602_3
  - boost=1.68.0=py36h8619c78_1001
  - boost-cpp=1.68.0=h11c811c_1000
  - boto3=1.7.84=py_0
  - botocore=1.10.84=py_0
  - bwidget=1.9.11=1
  - bzip2=1.0.6=h14c3975_1002
  - ca-certificates=2019.3.9=hecc5488_0
  - cachetools=2.1.0=py_0
  - cairo=1.16.0=ha4e643d_1000
  - certifi=2019.3.9=py36_0
  - cffi=1.12.3=py36h8022711_0
  - chardet=3.0.4=py36_1003
  - configargparse=0.13.0=py_1
  - cryptography=2.6.1=py36h72c5cf5_0
  - curl=7.64.1=hf8cf82a_0
  - datrie=0.7.1=py36h14c3975_0
  - decorator=4.4.0=py_0
  - docutils=0.14=py36_1001
  - dropbox=7.3.1=py36_0
  - expat=2.2.5=hf484d3e_1002
  - filechunkio=1.6=py36_0
  - fontconfig=2.13.1=he4413a7_1000
  - freetype=2.10.0=he983fc9_0
  - ftputil=3.2=py36_0
  - gcc_impl_linux-64=7.3.0=habb00fd_1
  - gcc_linux-64=7.3.0=h553295d_3
  - gettext=0.19.8.1=hc5be6a0_1002
  - gfortran_impl_linux-64=7.3.0=hdf63c60_1
  - gfortran_linux-64=7.3.0=h553295d_3
  - gitdb2=2.0.5=py_0
  - gitpython=2.1.11=py_0
  - glib=2.58.3=hf63aee3_1001
  - google-api-core=1.10.0=py36_0
  - google-auth=1.2.1=py_0
  - google-cloud-core=0.29.1=py_0
  - google-cloud-storage=1.15.0=py_0
  - google-resumable-media=0.3.2=py_0
  - googleapis-common-protos=1.5.9=py36_2
  - graphite2=1.3.13=hf484d3e_1000
  - graphviz=2.40.1=h0dab3d1_0
  - gsl=2.4=h294904e_1006
  - gxx_impl_linux-64=7.3.0=hdf63c60_1
  - gxx_linux-64=7.3.0=h553295d_3
  - harfbuzz=2.4.0=h37c48d4_0
  - hdf5=1.10.4=nompi_h3c11f04_1106
  - icu=58.2=hf484d3e_1000
  - idna=2.8=py36_1000
  - idna_ssl=1.1.0=py36_1000
  - jinja2=2.10.1=py_0
  - jmespath=0.9.4=py_0
  - jpeg=9c=h14c3975_1001
  - jsonschema=3.0.1=py36_0
  - krb5=1.16.3=h05b26f9_1001
  - libblas=3.8.0=8_openblas
  - libcblas=3.8.0=8_openblas
  - libcurl=7.64.1=hda55be3_0
  - libedit=3.1.20170329=hf8c457e_1001
  - libffi=3.2.1=he1b5a44_1006
  - libgcc-ng=8.2.0=hdf63c60_1
  - libgfortran-ng=7.3.0=hdf63c60_0
  - libiconv=1.15=h516909a_1005
  - liblapack=3.8.0=8_openblas
  - libpng=1.6.37=hed695b0_0
  - libprotobuf=3.7.1=h8b12597_0
  - libssh2=1.8.2=h22169c7_2
  - libstdcxx-ng=8.2.0=hdf63c60_1
  - libtiff=4.0.10=h648cc4a_1001
  - libtool=2.4.6=h14c3975_1002
  - libuuid=2.32.1=h14c3975_1000
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.9=h13577e0_0
  - make=4.2.1=h14c3975_2004
  - markupsafe=1.1.1=py36h14c3975_0
  - multidict=4.5.2=py36h14c3975_1000
  - ncurses=6.1=hf484d3e_1002
  - networkx=2.3=py_0
  - numpy=1.16.3=py36he5ce36f_0
  - openblas=0.3.6=h6e990d7_1
  - openssl=1.1.1b=h14c3975_1
  - pandas=0.24.2=py36hf484d3e_0
  - pandoc=2.7.2=0
  - pango=1.40.14=h4ea9474_1004
  - paramiko=2.4.2=py36_1000
  - pcre=8.41=hf484d3e_1003
  - pip=19.1=py36_0
  - pixman=0.34.0=h14c3975_1003
  - prettytable=0.7.2=py_2
  - protobuf=3.7.1=py36he1b5a44_0
  - psutil=5.6.2=py36h516909a_0
  - pthread-stubs=0.4=h14c3975_1001
  - pyasn1=0.4.4=py_1
  - pyasn1-modules=0.0.5=py36_0
  - pycparser=2.19=py36_1
  - pygraphviz=1.3.1=py36_0
  - pynacl=1.3.0=py36h14c3975_1000
  - pyrsistent=0.15.1=py36h516909a_0
  - pysftp=0.2.9=py36_0
  - python=3.6.7=h381d211_1004
  - python-dateutil=2.8.0=py_0
  - python-irodsclient=0.7.0=py_0
  - pytz=2019.1=py_0
  - pyyaml=5.1=py36h14c3975_0
  - r=3.5.1=r351_1000
  - r-askpass=1.1=r351h96ca727_0
  - r-assertthat=0.2.1=r351h6115d3f_0
  - r-backports=1.1.4=r351hcdcec82_0
  - r-base=3.5.1=h271c98b_1006
  - r-base64enc=0.1_3=r351h96ca727_1002
  - r-bh=1.69.0_1=r351h6115d3f_0
  - r-boot=1.3_22=r351_0
  - r-broom=0.5.2=r351h6115d3f_0
  - r-callr=3.2.0=r351h6115d3f_0
  - r-cellranger=1.1.0=r351h6115d3f_1001
  - r-class=7.3_15=r351h96ca727_1000
  - r-cli=1.1.0=r351h6115d3f_0
  - r-clipr=0.6.0=r351h6115d3f_0
  - r-cluster=2.0.9=r351h9bbef5b_0
  - r-codetools=0.2_16=r351h6115d3f_1000
  - r-colorspace=1.4_1=r351hcdcec82_0
  - r-crayon=1.3.4=r351h6115d3f_1001
  - r-curl=3.3=r351h96ca727_0
  - r-dbi=1.0.0=r351h6115d3f_1001
  - r-dbplyr=1.4.0=r351h6115d3f_0
  - r-digest=0.6.18=r351h96ca727_1000
  - r-dplyr=0.8.0.1=r351h29659fb_1000
  - r-ellipsis=0.1.0=r351h96ca727_0
  - r-evaluate=0.13=r351h6115d3f_1
  - r-fansi=0.4.0=r351h96ca727_1000
  - r-forcats=0.4.0=r351h6115d3f_0
  - r-foreign=0.8_71=r351h96ca727_1002
  - r-fs=1.3.0=r351h0357c0b_0
  - r-generics=0.0.2=r351h6115d3f_1001
  - r-ggplot2=3.1.1=r351h6115d3f_0
  - r-glue=1.3.1=r351hcdcec82_0
  - r-gtable=0.3.0=r351h6115d3f_0
  - r-haven=2.1.0=r351h29659fb_0
  - r-highr=0.8=r351h6115d3f_0
  - r-hms=0.4.2=r351h6115d3f_1000
  - r-htmltools=0.3.6=r351hf484d3e_1002
  - r-httr=1.4.0=r351h6115d3f_1000
  - r-jsonlite=1.6=r351h96ca727_1000
  - r-kernsmooth=2.23_15=r351ha65eedd_1002
  - r-knitr=1.22=r351h6115d3f_0
  - r-labeling=0.3=r351h6115d3f_1001
  - r-lattice=0.20_38=r351h96ca727_1000
  - r-lazyeval=0.2.2=r351hcdcec82_0
  - r-lubridate=1.7.4=r351h29659fb_1001
  - r-magrittr=1.5=r351h6115d3f_1001
  - r-markdown=0.9=r351h96ca727_1000
  - r-mass=7.3_51.4=r351hcdcec82_0
  - r-matrix=1.2_17=r351hcdcec82_0
  - r-mgcv=1.8_28=r351hcdcec82_0
  - r-mime=0.6=r351h96ca727_1000
  - r-modelr=0.1.4=r351h6115d3f_0
  - r-munsell=0.5.0=r351h6115d3f_1001
  - r-nlme=3.1_139=r351h9bbef5b_0
  - r-nnet=7.3_12=r351h96ca727_1002
  - r-openssl=1.3=r351h9c8475f_0
  - r-pillar=1.3.1=r351h6115d3f_1000
  - r-pkgconfig=2.0.2=r351h6115d3f_1001
  - r-plogr=0.2.0=r351h6115d3f_1001
  - r-plyr=1.8.4=r351h29659fb_1002
  - r-prettyunits=1.0.2=r351h6115d3f_1001
  - r-processx=3.3.0=r351hcdcec82_0
  - r-progress=1.2.0=r351h6115d3f_1002
  - r-ps=1.3.0=r351h96ca727_1000
  - r-purrr=0.3.2=r351hcdcec82_0
  - r-r6=2.4.0=r351h6115d3f_0
  - r-rcolorbrewer=1.1_2=r351h6115d3f_1001
  - r-rcpp=1.0.1=r351h0357c0b_0
  - r-readr=1.3.1=r351h29659fb_1000
  - r-readxl=1.3.1=r351h0357c0b_0
  - r-recommended=3.5.1=r351_1001
  - r-rematch=1.0.1=r351h6115d3f_1001
  - r-reprex=0.2.1=r351h6115d3f_1000
  - r-reshape2=1.4.3=r351h29659fb_1003
  - r-rlang=0.3.4=r351hcdcec82_0
  - r-rmarkdown=1.12=r351h6115d3f_0
  - r-rpart=4.1_15=r351hcdcec82_0
  - r-rstudioapi=0.10=r351h6115d3f_0
  - r-rvest=0.3.3=r351h6115d3f_0
  - r-scales=1.0.0=r351h29659fb_1001
  - r-selectr=0.4_1=r351h6115d3f_1000
  - r-spatial=7.3_11=r351h96ca727_1002
  - r-stringi=1.4.3=r351h0357c0b_0
  - r-stringr=1.4.0=r351h6115d3f_0
  - r-survival=2.44_1.1=r351hcdcec82_0
  - r-sys=3.2=r351hcdcec82_0
  - r-tibble=2.1.1=r351hcdcec82_0
  - r-tidyr=0.8.3=r351h0357c0b_0
  - r-tidyselect=0.2.5=r351h29659fb_1000
  - r-tidyverse=1.2.1=r351h6115d3f_1001
  - r-tinytex=0.12=r351h6115d3f_0
  - r-utf8=1.1.4=r351h96ca727_1000
  - r-viridislite=0.3.0=r351h6115d3f_1001
  - r-whisker=0.3_2=r351h6115d3f_1001
  - r-withr=2.1.2=r351h6115d3f_1000
  - r-xfun=0.6=r351h6115d3f_0
  - r-xml2=1.2.0=r351h29659fb_1002
  - r-yaml=2.2.0=r351h96ca727_1001
  - ratelimiter=1.2.0=py36_1000
  - readline=7.0=hf8c457e_1001
  - requests=2.13.0=py36_0
  - rsa=3.1.4=py36_0
  - s3transfer=0.1.13=py36_1001
  - setuptools=41.0.1=py36_0
  - six=1.12.0=py36_1000
  - smmap2=2.0.5=py_0
  - snakemake=5.3.0=2
  - snakemake-minimal=5.3.0=py_2
  - sqlite=3.26.0=h67949de_1001
  - sra-tools=2.9.1_1=h470a237_0
  - tk=8.6.9=h84994c4_1001
  - tktable=2.10=h14c3975_0
  - typing_extensions=3.7.2=py36_1000
  - urllib3=1.12=py36_0
  - wheel=0.33.1=py36_0
  - wrapt=1.11.1=py36h14c3975_0
  - xmlrunner=1.7.7=py_0
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.9=h516909a_1004
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.7=h14c3975_1000
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxpm=3.5.12=h14c3975_1002
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxt=1.1.5=h14c3975_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
  - yaml=0.1.7=h14c3975_1001
  - yarl=1.3.0=py36h14c3975_1000
  - zlib=1.2.11=h14c3975_1004
prefix: /home/sovacool/bin/anaconda3/envs/optiFit


## slurm-no-smk.yaml
name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _ipyw_jlab_nb_ext_conf=0.1.0=py37_0
  - alabaster=0.7.12=py37_0
  - anaconda=2019.03=py37_0
  - anaconda-client=1.7.2=py37_0
  - anaconda-navigator=1.9.7=py37_0
  - anaconda-project=0.8.2=py37_0
  - asn1crypto=0.24.0=py37_0
  - astroid=2.2.5=py37_0
  - astropy=3.1.2=py37h7b6447c_0
  - atomicwrites=1.3.0=py37_1
  - attrs=19.1.0=py37_1
  - babel=2.6.0=py37_0
  - backcall=0.1.0=py37_0
  - backports=1.0=py37_1
  - backports.os=0.1.1=py37_0
  - backports.shutil_get_terminal_size=1.0.0=py37_2
  - beautifulsoup4=4.7.1=py37_1
  - bitarray=0.8.3=py37h14c3975_0
  - bkcharts=0.2=py37_0
  - blas=1.0=mkl
  - bleach=3.1.0=py37_0
  - blosc=1.15.0=hd408876_0
  - bokeh=1.0.4=py37_0
  - boto=2.49.0=py37_0
  - bottleneck=1.2.1=py37h035aef0_1
  - bzip2=1.0.6=h14c3975_5
  - ca-certificates=2019.1.23=0
  - cairo=1.14.12=h8948797_3
  - certifi=2019.3.9=py37_0
  - cffi=1.12.2=py37h2e261b9_1
  - chardet=3.0.4=py37_1
  - click=7.0=py37_0
  - cloudpickle=0.8.0=py37_0
  - clyent=1.2.2=py37_1
  - colorama=0.4.1=py37_0
  - conda=4.6.14=py37_0
  - conda-build=3.17.8=py37_0
  - conda-env=2.6.0=1
  - conda-verify=3.1.1=py37_0
  - contextlib2=0.5.5=py37_0
  - cryptography=2.6.1=py37h1ba5d50_0
  - curl=7.64.0=hbc83047_2
  - cycler=0.10.0=py37_0
  - cython=0.29.6=py37he6710b0_0
  - cytoolz=0.9.0.1=py37h14c3975_1
  - dask=1.1.4=py37_1
  - dask-core=1.1.4=py37_1
  - dbus=1.13.6=h746ee38_0
  - decorator=4.4.0=py37_1
  - defusedxml=0.5.0=py37_1
  - distributed=1.26.0=py37_1
  - docutils=0.14=py37_0
  - entrypoints=0.3=py37_0
  - et_xmlfile=1.0.1=py37_0
  - expat=2.2.6=he6710b0_0
  - fastcache=1.0.2=py37h14c3975_2
  - filelock=3.0.10=py37_0
  - flask=1.0.2=py37_1
  - fontconfig=2.13.0=h9420a91_0
  - freetype=2.9.1=h8a8886c_1
  - fribidi=1.0.5=h7b6447c_0
  - future=0.17.1=py37_0
  - get_terminal_size=1.0.0=haa9412d_0
  - gevent=1.4.0=py37h7b6447c_0
  - glib=2.56.2=hd408876_0
  - glob2=0.6=py37_1
  - gmp=6.1.2=h6c8ec71_1
  - gmpy2=2.0.8=py37h10f8cd9_2
  - graphite2=1.3.13=h23475e2_0
  - greenlet=0.4.15=py37h7b6447c_0
  - gst-plugins-base=1.14.0=hbbd80ab_1
  - gstreamer=1.14.0=hb453b48_1
  - h5py=2.9.0=py37h7918eee_0
  - harfbuzz=1.8.8=hffaf4a1_0
  - hdf5=1.10.4=hb1b8bf9_0
  - heapdict=1.0.0=py37_2
  - html5lib=1.0.1=py37_0
  - icu=58.2=h9c2bf20_1
  - idna=2.8=py37_0
  - imageio=2.5.0=py37_0
  - imagesize=1.1.0=py37_0
  - importlib_metadata=0.8=py37_0
  - intel-openmp=2019.3=199
  - ipykernel=5.1.0=py37h39e3cac_0
  - ipython=7.4.0=py37h39e3cac_0
  - ipython_genutils=0.2.0=py37_0
  - ipywidgets=7.4.2=py37_0
  - isort=4.3.16=py37_0
  - itsdangerous=1.1.0=py37_0
  - jbig=2.1=hdba287a_0
  - jdcal=1.4=py37_0
  - jedi=0.13.3=py37_0
  - jeepney=0.4=py37_0
  - jinja2=2.10=py37_0
  - jpeg=9b=h024ee3a_2
  - jsonschema=3.0.1=py37_0
  - jupyter=1.0.0=py37_7
  - jupyter_client=5.2.4=py37_0
  - jupyter_console=6.0.0=py37_0
  - jupyter_core=4.4.0=py37_0
  - jupyterlab=0.35.4=py37hf63ae98_0
  - jupyterlab_server=0.2.0=py37_0
  - keyring=18.0.0=py37_0
  - kiwisolver=1.0.1=py37hf484d3e_0
  - krb5=1.16.1=h173b8e3_7
  - lazy-object-proxy=1.3.1=py37h14c3975_2
  - libarchive=3.3.3=h5d8350f_5
  - libcurl=7.64.0=h20c2e04_2
  - libedit=3.1.20181209=hc058e9b_0
  - 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_2
  - libpng=1.6.36=hbc83047_0
  - libsodium=1.0.16=h1bed415_0
  - libssh2=1.8.0=h1ba5d50_4
  - libstdcxx-ng=8.2.0=hdf63c60_1
  - libtiff=4.0.10=h2733197_2
  - libtool=2.4.6=h7b6447c_5
  - libuuid=1.0.3=h1bed415_2
  - libxcb=1.13=h1bed415_1
  - libxml2=2.9.9=he19cac6_0
  - libxslt=1.1.33=h7d1a2b0_0
  - llvmlite=0.28.0=py37hd408876_0
  - locket=0.2.0=py37_1
  - lxml=4.3.2=py37hefd8a0e_0
  - lz4-c=1.8.1.2=h14c3975_0
  - lzo=2.10=h49e0be7_2
  - markupsafe=1.1.1=py37h7b6447c_0
  - matplotlib=3.0.3=py37h5429711_0
  - mccabe=0.6.1=py37_1
  - mistune=0.8.4=py37h7b6447c_0
  - mkl=2019.3=199
  - mkl-service=1.1.2=py37he904b0f_5
  - mkl_fft=1.0.10=py37ha843d7b_0
  - mkl_random=1.0.2=py37hd81dba3_0
  - more-itertools=6.0.0=py37_0
  - mpc=1.1.0=h10f8cd9_1
  - mpfr=4.0.1=hdf1c602_3
  - mpmath=1.1.0=py37_0
  - msgpack-python=0.6.1=py37hfd86e86_1
  - multipledispatch=0.6.0=py37_0
  - navigator-updater=0.2.1=py37_0
  - nbconvert=5.4.1=py37_3
  - nbformat=4.4.0=py37_0
  - ncurses=6.1=he6710b0_1
  - networkx=2.2=py37_1
  - nltk=3.4=py37_1
  - nose=1.3.7=py37_2
  - notebook=5.7.8=py37_0
  - numba=0.43.1=py37h962f231_0
  - numexpr=2.6.9=py37h9e4a6bb_0
  - numpy=1.16.2=py37h7e9f1db_0
  - numpy-base=1.16.2=py37hde5b4d6_0
  - numpydoc=0.8.0=py37_0
  - olefile=0.46=py37_0
  - openpyxl=2.6.1=py37_1
  - openssl=1.1.1b=h7b6447c_1
  - packaging=19.0=py37_0
  - pandas=0.24.2=py37he6710b0_0
  - pandoc=2.2.3.2=0
  - pandocfilters=1.4.2=py37_1
  - pango=1.42.4=h049681c_0
  - parso=0.3.4=py37_0
  - partd=0.3.10=py37_1
  - patchelf=0.9=he6710b0_3
  - path.py=11.5.0=py37_0
  - pathlib2=2.3.3=py37_0
  - patsy=0.5.1=py37_0
  - pcre=8.43=he6710b0_0
  - pep8=1.7.1=py37_0
  - pexpect=4.6.0=py37_0
  - pickleshare=0.7.5=py37_0
  - pillow=5.4.1=py37h34e0f95_0
  - pip=19.0.3=py37_0
  - pixman=0.38.0=h7b6447c_0
  - pkginfo=1.5.0.1=py37_0
  - pluggy=0.9.0=py37_0
  - ply=3.11=py37_0
  - prometheus_client=0.6.0=py37_0
  - prompt_toolkit=2.0.9=py37_0
  - psutil=5.6.1=py37h7b6447c_0
  - ptyprocess=0.6.0=py37_0
  - py=1.8.0=py37_0
  - py-lief=0.9.0=py37h7725739_2
  - pycodestyle=2.5.0=py37_0
  - pycosat=0.6.3=py37h14c3975_0
  - pycparser=2.19=py37_0
  - pycrypto=2.6.1=py37h14c3975_9
  - pycurl=7.43.0.2=py37h1ba5d50_0
  - pyflakes=2.1.1=py37_0
  - pygments=2.3.1=py37_0
  - pylint=2.3.1=py37_0
  - pyodbc=4.0.26=py37he6710b0_0
  - pyopenssl=19.0.0=py37_0
  - pyparsing=2.3.1=py37_0
  - pyqt=5.9.2=py37h05f1152_2
  - pyrsistent=0.14.11=py37h7b6447c_0
  - pysocks=1.6.8=py37_0
  - pytables=3.5.1=py37h71ec239_0
  - pytest=4.3.1=py37_0
  - pytest-arraydiff=0.3=py37h39e3cac_0
  - pytest-astropy=0.5.0=py37_0
  - pytest-doctestplus=0.3.0=py37_0
  - pytest-openfiles=0.3.2=py37_0
  - pytest-remotedata=0.3.1=py37_0
  - python=3.7.3=h0371630_0
  - python-dateutil=2.8.0=py37_0
  - python-libarchive-c=2.8=py37_6
  - pytz=2018.9=py37_0
  - pywavelets=1.0.2=py37hdd07704_0
  - pyyaml=5.1=py37h7b6447c_0
  - pyzmq=18.0.0=py37he6710b0_0
  - qt=5.9.7=h5867ecd_1
  - qtawesome=0.5.7=py37_1
  - qtconsole=4.4.3=py37_0
  - qtpy=1.7.0=py37_1
  - readline=7.0=h7b6447c_5
  - requests=2.21.0=py37_0
  - rope=0.12.0=py37_0
  - ruamel_yaml=0.15.46=py37h14c3975_0
  - scikit-image=0.14.2=py37he6710b0_0
  - scikit-learn=0.20.3=py37hd81dba3_0
  - scipy=1.2.1=py37h7c811a0_0
  - seaborn=0.9.0=py37_0
  - secretstorage=3.1.1=py37_0
  - send2trash=1.5.0=py37_0
  - setuptools=40.8.0=py37_0
  - simplegeneric=0.8.1=py37_2
  - singledispatch=3.4.0.3=py37_0
  - sip=4.19.8=py37hf484d3e_0
  - six=1.12.0=py37_0
  - snappy=1.1.7=hbae5bb6_3
  - snowballstemmer=1.2.1=py37_0
  - sortedcollections=1.1.2=py37_0
  - sortedcontainers=2.1.0=py37_0
  - soupsieve=1.8=py37_0
  - sphinx=1.8.5=py37_0
  - sphinxcontrib=1.0=py37_1
  - sphinxcontrib-websupport=1.1.0=py37_1
  - spyder=3.3.3=py37_0
  - spyder-kernels=0.4.2=py37_0
  - sqlalchemy=1.3.1=py37h7b6447c_0
  - sqlite=3.27.2=h7b6447c_0
  - statsmodels=0.9.0=py37h035aef0_0
  - sympy=1.3=py37_0
  - tblib=1.3.2=py37_0
  - terminado=0.8.1=py37_1
  - testpath=0.4.2=py37_0
  - tk=8.6.8=hbc83047_0
  - toolz=0.9.0=py37_0
  - tornado=6.0.2=py37h7b6447c_0
  - tqdm=4.31.1=py37_1
  - traitlets=4.3.2=py37_0
  - unicodecsv=0.14.1=py37_0
  - unixodbc=2.3.7=h14c3975_0
  - urllib3=1.24.1=py37_0
  - wcwidth=0.1.7=py37_0
  - webencodings=0.5.1=py37_1
  - werkzeug=0.14.1=py37_0
  - wheel=0.33.1=py37_0
  - widgetsnbextension=3.4.2=py37_0
  - wrapt=1.11.1=py37h7b6447c_0
  - wurlitzer=1.0.2=py37_0
  - xlrd=1.2.0=py37_0
  - xlsxwriter=1.1.5=py37_0
  - xlwt=1.3.0=py37_0
  - xz=5.2.4=h14c3975_4
  - yaml=0.1.7=had09818_2
  - zeromq=4.3.1=he6710b0_3
  - zict=0.1.4=py37_0
  - zipp=0.3.3=py37_1
  - zlib=1.2.11=h7b6447c_3
  - zstd=1.3.7=h0b5b093_0
prefix: /home/sovacool/bin/anaconda3


## slurm-with-smk.yaml
name: test
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - aioeasywebdav=2.2.0=py36_0
  - aiohttp=3.5.4=py36h14c3975_0
  - appdirs=1.4.3=py_1
  - asn1crypto=0.24.0=py36_1003
  - async-timeout=3.0.1=py_1000
  - attrs=19.1.0=py_0
  - bcrypt=3.1.4=py36h470a237_0
  - boto3=1.9.159=py_0
  - botocore=1.12.159=py_0
  - ca-certificates=2019.3.9=hecc5488_0
  - cachetools=2.1.0=py_0
  - cairo=1.16.0=ha4e643d_1000
  - certifi=2019.3.9=py36_0
  - cffi=1.12.3=py36h8022711_0
  - chardet=3.0.4=py36_1003
  - configargparse=0.13.0=py_1
  - cryptography=2.6.1=py36h72c5cf5_0
  - datrie=0.7.1=py36h14c3975_0
  - decorator=4.4.0=py_0
  - docutils=0.14=py36_1001
  - dropbox=9.3.0=py_0
  - expat=2.2.5=hf484d3e_1002
  - filechunkio=1.8=py_2
  - fontconfig=2.13.1=he4413a7_1000
  - freetype=2.10.0=he983fc9_0
  - ftputil=3.4=py_0
  - gettext=0.19.8.1=hc5be6a0_1002
  - gitdb2=2.0.5=py_0
  - gitpython=2.1.11=py_0
  - glib=2.58.3=hf63aee3_1001
  - google-api-core=1.11.0=py36_0
  - google-auth=1.6.3=py_0
  - google-cloud-core=1.0.1=py_0
  - google-cloud-storage=1.16.0=py_0
  - google-resumable-media=0.3.2=py_0
  - googleapis-common-protos=1.6.0=py36_0
  - graphite2=1.3.13=hf484d3e_1000
  - graphviz=2.38.0=hf68f40c_1011
  - harfbuzz=2.4.0=h37c48d4_0
  - icu=58.2=hf484d3e_1000
  - idna=2.8=py36_1000
  - idna_ssl=1.1.0=py36_1000
  - jinja2=2.10.1=py_0
  - jmespath=0.9.4=py_0
  - jpeg=9c=h14c3975_1001
  - jsonschema=3.0.1=py36_0
  - libblas=3.8.0=10_openblas
  - libcblas=3.8.0=10_openblas
  - libffi=3.2.1=he1b5a44_1006
  - libgcc-ng=8.2.0=hdf63c60_1
  - libgfortran-ng=7.3.0=hdf63c60_0
  - libiconv=1.15=h516909a_1005
  - liblapack=3.8.0=10_openblas
  - libpng=1.6.37=hed695b0_0
  - libprotobuf=3.7.1=h8b12597_0
  - libstdcxx-ng=8.2.0=hdf63c60_1
  - libtiff=4.0.10=h57b8799_1003
  - libtool=2.4.6=h14c3975_1002
  - libuuid=2.32.1=h14c3975_1000
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.9=h13577e0_0
  - lz4-c=1.8.3=he1b5a44_1001
  - markupsafe=1.1.1=py36h14c3975_0
  - multidict=4.5.2=py36h14c3975_1000
  - ncurses=6.1=hf484d3e_1002
  - networkx=2.3=py_0
  - numpy=1.16.4=py36h95a1406_0
  - openblas=0.3.6=h6e990d7_2
  - openssl=1.1.1b=h14c3975_1
  - pandas=0.24.2=py36hb3f55d8_0
  - pango=1.40.14=h4ea9474_1004
  - paramiko=2.4.2=py36_1000
  - pcre=8.41=hf484d3e_1003
  - pip=19.1=py36_0
  - pixman=0.34.0=h14c3975_1003
  - prettytable=0.7.2=py_2
  - protobuf=3.7.1=py36he1b5a44_0
  - psutil=5.6.2=py36h516909a_0
  - pthread-stubs=0.4=h14c3975_1001
  - pyasn1=0.4.5=py_0
  - pyasn1-modules=0.2.5=py_0
  - pycparser=2.19=py36_1
  - pygraphviz=1.5=py36h14c3975_1000
  - pynacl=1.3.0=py36h14c3975_1000
  - pyopenssl=19.0.0=py36_0
  - pyrsistent=0.15.2=py36h516909a_0
  - pysftp=0.2.9=py_1
  - pysocks=1.7.0=py36_0
  - python=3.6.7=h381d211_1004
  - python-dateutil=2.8.0=py_0
  - python-irodsclient=0.7.0=py_0
  - pytz=2019.1=py_0
  - pyyaml=5.1=py36h14c3975_0
  - ratelimiter=1.2.0=py36_1000
  - readline=7.0=hf8c457e_1001
  - requests=2.22.0=py36_0
  - rsa=3.4.2=py_1
  - s3transfer=0.2.0=py36_0
  - setuptools=41.0.1=py36_0
  - six=1.12.0=py36_1000
  - smmap2=2.0.5=py_0
  - snakemake=5.5.0=0
  - snakemake-minimal=5.5.0=py_0
  - sqlite=3.28.0=h8b20d00_0
  - tk=8.6.9=h84994c4_1001
  - typing_extensions=3.7.2=py36_1000
  - urllib3=1.24.3=py36_0
  - wheel=0.33.4=py36_0
  - wrapt=1.11.1=py36h516909a_0
  - xmlrunner=1.7.7=py_0
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.9=h516909a_1004
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.7=h14c3975_1000
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxpm=3.5.12=h14c3975_1002
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxt=1.1.5=h14c3975_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
  - yaml=0.1.7=h14c3975_1001
  - yarl=1.3.0=py36h14c3975_1000
  - zlib=1.2.11=h14c3975_1004
  - zstd=1.4.0=h3b9ef0a_0
prefix: /home/sovacool/bin/anaconda3/envs/test


## Snakefile
rule touch:
	output:
		"file.txt"
	shell:
		"touch {output}"

## submit-pbs.sh
#PBS -N smk ## Name of the job for the scheduler
#PBS -A pschloss_fluxod ## name of the allocation (who is paying for the compute time)
#PBS -q fluxod ## name of the queue to submit the job to. Will match the suffix on allocation name
#PBS -l nodes=1:ppn=1,pmem=100MB,walltime=1:00    ## resource reservation  max walltime = 672 hours
#PBS -l qos=flux		## quality of service DO NOT CHANGE THIS
#PBS -M		## send email notifications to umich email listed
#PBS -m a                ## when to send email a=abort b=job begin e=job end
#PBS -j oe                 ## join output & error files to same file, and send to the email listed above
#PBS -V                 ## IMPORTANT always use this. send environment setup to node job will be run on
#
#  Include the next three lines always
if [ "x${PBS_NODEFILE}" != "x" ] ; then
   cat $PBS_NODEFILE   # contains a list of the CPUs you were using if run with PBS
fi

# Always add this line to change to the working directory of the program. Otherwise
# the script will be run from the users /home directory
cd $PBS_O_WORKDIR
echo $PBS_O_WORKDIR

snakemake


## submit-slurm.sh
#!/bin/bash

##################
####  Slurm preamble

#### #### ####  These are the most frequently changing options

####  Job name
#SBATCH --job-name=smk

####  Request resources here
####    These are typically, number of processors, amount of memory,
####    an the amount of time a job requires.  May include processor
####    type, too.

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=200m
#SBATCH --time=1:00


####  Slurm account and partition specification here
####    These will change if you work on multiple projects, or need
####    special hardware, like large memory nodes or GPUs.

#SBATCH --account=test
#SBATCH --partition=standard

#### #### ####  These are the least frequently changing options

####  Your e-mail address and when you want e-mail

#SBATCH --mail-user=
#SBATCH --mail-type=BEGIN,END

# Add a note here to say what software modules should be loaded.
# for this job to run successfully.
# It will be convenient if you give the actual load command(s), e.g.,
#
# module load R

####  End Slurm preamble
##################


####  Commands your job should run follow this line

snakemake

##  If you copied any files to /tmp, make sure you delete them here!
	name: base
	channels:
	- conda-forge
	- bioconda
	- defaults
	dependencies:
	- _ipyw_jlab_nb_ext_conf=0.1.0=py37_0
	- alabaster=0.7.11=py37_0
	- anaconda=custom=py37_0
	- anaconda-client=1.7.2=py37_0
	- anaconda-navigator=1.9.2=py37_0
	- anaconda-project=0.8.2=py37_0
	- appdirs=1.4.3=py37h28b3542_0
	- asn1crypto=0.24.0=py37_0
	- astroid=2.0.4=py37_0
	- astropy=3.0.4=py37h14c3975_0
	- atomicwrites=1.2.1=py37_0
	- attrs=18.2.0=py37h28b3542_0
	- automat=0.7.0=py37_0
	- babel=2.6.0=py37_0
	- backcall=0.1.0=py37_0
	- backports=1.0=py37_1
	- backports.shutil_get_terminal_size=1.0.0=py37_2
	- beautifulsoup4=4.6.3=py37_0
	- bitarray=0.8.3=py37h14c3975_0
	- bkcharts=0.2=py37_0
	- blas=1.0=mkl
	- blaze=0.11.3=py37_0
	- bleach=2.1.4=py37_0
	- blosc=1.14.4=hdbcaa40_0
	- bokeh=0.13.0=py37_0
	- boto=2.49.0=py37_0
	- bottleneck=1.2.1=py37h035aef0_1
	- bzip2=1.0.6=h14c3975_5
	- ca-certificates=2019.5.15=0
	- cairo=1.14.12=h8948797_3
	- certifi=2019.3.9=py37_0
	- cffi=1.11.5=py37he75722e_1
	- chardet=3.0.4=py37_1
	- click=6.7=py37_0
	- cloudpickle=0.5.5=py37_0
	- clyent=1.2.2=py37_1
	- colorama=0.3.9=py37_0
	- conda=4.6.14=py37_0
	- conda-build=3.15.1=py37_0
	- conda-env=2.6.0=1
	- constantly=15.1.0=py37h28b3542_0
	- contextlib2=0.5.5=py37_0
	- cryptography=2.6.1=py37h1ba5d50_0
	- curl=7.64.1=hbc83047_0
	- cycler=0.10.0=py37_0
	- cython=0.28.5=py37hf484d3e_0
	- cytoolz=0.9.0.1=py37h14c3975_1
	- dask=0.19.1=py37_0
	- dask-core=0.19.1=py37_0
	- datashape=0.5.4=py37_1
	- dbus=1.13.2=h714fa37_1
	- decorator=4.3.0=py37_0
	- defusedxml=0.5.0=py37_1
	- distributed=1.23.1=py37_0
	- docutils=0.14=py37_0
	- entrypoints=0.2.3=py37_2
	- et_xmlfile=1.0.1=py37_0
	- expat=2.2.6=he6710b0_0
	- fastcache=1.0.2=py37h14c3975_2
	- filelock=3.0.8=py37_0
	- flask=1.0.2=py37_1
	- flask-cors=3.0.6=py37_0
	- fontconfig=2.13.0=h9420a91_0
	- freetype=2.9.1=h8a8886c_1
	- fribidi=1.0.5=h7b6447c_0
	- get_terminal_size=1.0.0=haa9412d_0
	- gevent=1.3.6=py37h7b6447c_0
	- glib=2.56.2=hd408876_0
	- glob2=0.6=py37_0
	- gmp=6.1.2=h6c8ec71_1
	- gmpy2=2.0.8=py37h10f8cd9_2
	- graphite2=1.3.12=h23475e2_2
	- greenlet=0.4.15=py37h7b6447c_0
	- gst-plugins-base=1.14.0=hbbd80ab_1
	- gstreamer=1.14.0=hb453b48_1
	- h5py=2.8.0=py37h989c5e5_3
	- harfbuzz=1.8.8=hffaf4a1_0
	- hdf5=1.10.2=hba1933b_1
	- heapdict=1.0.0=py37_2
	- html5lib=1.0.1=py37_0
	- hyperlink=18.0.0=py37_0
	- icu=58.2=h9c2bf20_1
	- idna=2.7=py37_0
	- imageio=2.4.1=py37_0
	- imagesize=1.1.0=py37_0
	- incremental=17.5.0=py37_0
	- intel-openmp=2019.0=118
	- ipykernel=4.9.0=py37_1
	- ipython=6.5.0=py37_0
	- ipython_genutils=0.2.0=py37_0
	- ipywidgets=7.4.1=py37_0
	- isort=4.3.4=py37_0
	- itsdangerous=0.24=py37_1
	- jbig=2.1=hdba287a_0
	- jdcal=1.4=py37_0
	- jedi=0.12.1=py37_0
	- jeepney=0.3.1=py37_0
	- jinja2=2.10=py37_0
	- jpeg=9b=h024ee3a_2
	- jsonschema=2.6.0=py37_0
	- jupyter=1.0.0=py37_7
	- jupyter_client=5.2.3=py37_0
	- jupyter_console=5.2.0=py37_1
	- jupyter_core=4.4.0=py37_0
	- jupyterlab=0.34.9=py37_0
	- jupyterlab_launcher=0.13.1=py37_0
	- keyring=13.2.1=py37_0
	- kiwisolver=1.0.1=py37hf484d3e_0
	- krb5=1.16.1=h173b8e3_7
	- lazy-object-proxy=1.3.1=py37h14c3975_2
	- libcurl=7.64.1=h20c2e04_0
	- 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
	- libpng=1.6.37=hbc83047_0
	- libsodium=1.0.16=h1bed415_0
	- libssh2=1.8.2=h1ba5d50_0
	- libstdcxx-ng=8.2.0=hdf63c60_1
	- libtiff=4.0.9=he85c1e1_2
	- libtool=2.4.6=h544aabb_3
	- libuuid=1.0.3=h1bed415_2
	- libxcb=1.13=h1bed415_1
	- libxml2=2.9.8=h26e45fe_1
	- libxslt=1.1.32=h1312cb7_0
	- llvmlite=0.24.0=py37hdbcaa40_0
	- locket=0.2.0=py37_1
	- lxml=4.2.5=py37hefd8a0e_0
	- lzo=2.10=h49e0be7_2
	- markupsafe=1.0=py37h14c3975_1
	- matplotlib=2.2.3=py37hb69df0a_0
	- mccabe=0.6.1=py37_1
	- mistune=0.8.3=py37h14c3975_1
	- mkl=2019.0=118
	- mkl-service=1.1.2=py37h90e4bf4_5
	- mkl_fft=1.0.4=py37h4414c95_1
	- mkl_random=1.0.1=py37h4414c95_1
	- more-itertools=4.3.0=py37_0
	- mpc=1.1.0=h10f8cd9_1
	- mpfr=4.0.1=hdf1c602_3
	- mpmath=1.0.0=py37_2
	- msgpack-python=0.5.6=py37h6bb024c_1
	- multipledispatch=0.6.0=py37_0
	- navigator-updater=0.2.1=py37_0
	- nbconvert=5.4.0=py37_1
	- nbformat=4.4.0=py37_0
	- ncurses=6.1=hf484d3e_0
	- networkx=2.1=py37_0
	- nltk=3.3.0=py37_0
	- nose=1.3.7=py37_2
	- notebook=5.6.0=py37_0
	- numba=0.39.0=py37h04863e7_0
	- numexpr=2.6.8=py37hd89afb7_0
	- numpy=1.15.1=py37h1d66e8a_0
	- numpy-base=1.15.1=py37h81de0dd_0
	- numpydoc=0.8.0=py37_0
	- odo=0.5.1=py37_0
	- olefile=0.46=py37_0
	- openpyxl=2.5.6=py37_0
	- openssl=1.1.1c=h7b6447c_1
	- packaging=17.1=py37_0
	- pandas=0.23.4=py37h04863e7_0
	- pandoc=1.19.2.1=hea2e7c5_1
	- pandocfilters=1.4.2=py37_1
	- pango=1.42.4=h049681c_0
	- parso=0.3.1=py37_0
	- partd=0.3.8=py37_0
	- patchelf=0.9=hf484d3e_2
	- path.py=11.1.0=py37_0
	- pathlib2=2.3.2=py37_0
	- patsy=0.5.0=py37_0
	- pcre=8.42=h439df22_0
	- pep8=1.7.1=py37_0
	- pexpect=4.6.0=py37_0
	- pickleshare=0.7.4=py37_0
	- pillow=5.2.0=py37heded4f4_0
	- pip=10.0.1=py37_0
	- pixman=0.34.0=hceecf20_3
	- pkginfo=1.4.2=py37_1
	- pluggy=0.7.1=py37h28b3542_0
	- ply=3.11=py37_0
	- prometheus_client=0.3.1=py37h28b3542_0
	- prompt_toolkit=1.0.15=py37_0
	- psutil=5.4.7=py37h14c3975_0
	- ptyprocess=0.6.0=py37_0
	- py=1.6.0=py37_0
	- pyasn1=0.4.4=py37h28b3542_0
	- pyasn1-modules=0.2.2=py37_0
	- pycodestyle=2.4.0=py37_0
	- pycosat=0.6.3=py37h14c3975_0
	- pycparser=2.18=py37_1
	- pycrypto=2.6.1=py37h14c3975_9
	- pycurl=7.43.0.2=py37h1ba5d50_0
	- pyflakes=2.0.0=py37_0
	- pygments=2.2.0=py37_0
	- pylint=2.1.1=py37_0
	- pyodbc=4.0.24=py37he6710b0_0
	- pyopenssl=18.0.0=py37_0
	- pyparsing=2.2.0=py37_1
	- pyqt=5.9.2=py37h05f1152_2
	- pysocks=1.6.8=py37_0
	- pytables=3.4.4=py37ha205bf6_0
	- pytest=3.8.0=py37_0
	- pytest-arraydiff=0.2=py37h39e3cac_0
	- pytest-astropy=0.4.0=py37_0
	- pytest-doctestplus=0.1.3=py37_0
	- pytest-openfiles=0.3.0=py37_0
	- pytest-remotedata=0.3.0=py37_0
	- python=3.7.2=h0371630_0
	- python-dateutil=2.7.3=py37_0
	- pytz=2018.5=py37_0
	- pywavelets=1.0.0=py37hdd07704_0
	- pyyaml=3.13=py37h14c3975_0
	- pyzmq=17.1.2=py37h14c3975_0
	- qt=5.9.7=h5867ecd_1
	- qtawesome=0.4.4=py37_0
	- qtconsole=4.4.1=py37_0
	- qtpy=1.5.0=py37_0
	- readline=7.0=h7b6447c_5
	- requests=2.19.1=py37_0
	- rope=0.11.0=py37_0
	- ruamel_yaml=0.15.46=py37h14c3975_0
	- scikit-image=0.14.0=py37hf484d3e_1
	- scikit-learn=0.19.2=py37h4989274_0
	- scipy=1.1.0=py37hfa4b5c9_1
	- seaborn=0.9.0=py37_0
	- secretstorage=3.1.0=py37_0
	- send2trash=1.5.0=py37_0
	- service_identity=17.0.0=py37h28b3542_0
	- setuptools=40.2.0=py37_0
	- simplegeneric=0.8.1=py37_2
	- singledispatch=3.4.0.3=py37_0
	- sip=4.19.8=py37hf484d3e_0
	- six=1.11.0=py37_1
	- snappy=1.1.7=hbae5bb6_3
	- snowballstemmer=1.2.1=py37_0
	- sortedcollections=1.0.1=py37_0
	- sortedcontainers=2.0.5=py37_0
	- sphinx=1.7.9=py37_0
	- sphinxcontrib=1.0=py37_1
	- sphinxcontrib-websupport=1.1.0=py37_1
	- spyder=3.3.1=py37_1
	- spyder-kernels=0.2.6=py37_0
	- sqlalchemy=1.2.11=py37h7b6447c_0
	- sqlite=3.26.0=h7b6447c_0
	- statsmodels=0.9.0=py37h035aef0_0
	- sympy=1.2=py37_0
	- tblib=1.3.2=py37_0
	- terminado=0.8.1=py37_1
	- testpath=0.3.1=py37_0
	- tk=8.6.8=hbc83047_0
	- toolz=0.9.0=py37_0
	- tornado=5.1=py37h14c3975_0
	- tqdm=4.26.0=py37h28b3542_0
	- traitlets=4.3.2=py37_0
	- twisted=18.7.0=py37h14c3975_1
	- unicodecsv=0.14.1=py37_0
	- unixodbc=2.3.7=h14c3975_0
	- urllib3=1.23=py37_0
	- wcwidth=0.1.7=py37_0
	- webencodings=0.5.1=py37_1
	- werkzeug=0.14.1=py37_0
	- wheel=0.31.1=py37_0
	- widgetsnbextension=3.4.1=py37_0
	- wrapt=1.10.11=py37h14c3975_2
	- xlrd=1.1.0=py37_1
	- xlsxwriter=1.1.0=py37_0
	- xlwt=1.3.0=py37_0
	- xz=5.2.4=h14c3975_4
	- yaml=0.1.7=had09818_2
	- zeromq=4.2.5=hf484d3e_1
	- zict=0.1.3=py37_0
	- zlib=1.2.11=ha838bed_2
	- zope=1.0=py37_1
	- zope.interface=4.5.0=py37h14c3975_0
	- pip:
	- arrow==0.12.1
	- binaryornot==0.4.4
	- cookiecutter==1.6.0
	- future==0.17.1
	- jinja2-time==0.2.0
	- poyo==0.4.2
	- whichcraft==0.5.2
	prefix: /home/sovacool/bin/anaconda3
	name: optiFit
	channels:
	- conda-forge
	- bioconda
	- defaults
	dependencies:
	- _r-mutex=1.0.0=anacondar_1
	- aioeasywebdav=2.2.0=py36_0
	- aiohttp=3.5.4=py36h14c3975_0
	- appdirs=1.4.3=py_1
	- asn1crypto=0.24.0=py36_1003
	- async-timeout=3.0.1=py_1000
	- attrs=19.1.0=py_0
	- bcrypt=3.1.4=py36h470a237_0
	- binutils_impl_linux-64=2.31.1=h6176602_1
	- binutils_linux-64=2.31.1=h6176602_3
	- boost=1.68.0=py36h8619c78_1001
	- boost-cpp=1.68.0=h11c811c_1000
	- boto3=1.7.84=py_0
	- botocore=1.10.84=py_0
	- bwidget=1.9.11=1
	- bzip2=1.0.6=h14c3975_1002
	- ca-certificates=2019.3.9=hecc5488_0
	- cachetools=2.1.0=py_0
	- cairo=1.16.0=ha4e643d_1000
	- certifi=2019.3.9=py36_0
	- cffi=1.12.3=py36h8022711_0
	- chardet=3.0.4=py36_1003
	- configargparse=0.13.0=py_1
	- cryptography=2.6.1=py36h72c5cf5_0
	- curl=7.64.1=hf8cf82a_0
	- datrie=0.7.1=py36h14c3975_0
	- decorator=4.4.0=py_0
	- docutils=0.14=py36_1001
	- dropbox=7.3.1=py36_0
	- expat=2.2.5=hf484d3e_1002
	- filechunkio=1.6=py36_0
	- fontconfig=2.13.1=he4413a7_1000
	- freetype=2.10.0=he983fc9_0
	- ftputil=3.2=py36_0
	- gcc_impl_linux-64=7.3.0=habb00fd_1
	- gcc_linux-64=7.3.0=h553295d_3
	- gettext=0.19.8.1=hc5be6a0_1002
	- gfortran_impl_linux-64=7.3.0=hdf63c60_1
	- gfortran_linux-64=7.3.0=h553295d_3
	- gitdb2=2.0.5=py_0
	- gitpython=2.1.11=py_0
	- glib=2.58.3=hf63aee3_1001
	- google-api-core=1.10.0=py36_0
	- google-auth=1.2.1=py_0
	- google-cloud-core=0.29.1=py_0
	- google-cloud-storage=1.15.0=py_0
	- google-resumable-media=0.3.2=py_0
	- googleapis-common-protos=1.5.9=py36_2
	- graphite2=1.3.13=hf484d3e_1000
	- graphviz=2.40.1=h0dab3d1_0
	- gsl=2.4=h294904e_1006
	- gxx_impl_linux-64=7.3.0=hdf63c60_1
	- gxx_linux-64=7.3.0=h553295d_3
	- harfbuzz=2.4.0=h37c48d4_0
	- hdf5=1.10.4=nompi_h3c11f04_1106
	- icu=58.2=hf484d3e_1000
	- idna=2.8=py36_1000
	- idna_ssl=1.1.0=py36_1000
	- jinja2=2.10.1=py_0
	- jmespath=0.9.4=py_0
	- jpeg=9c=h14c3975_1001
	- jsonschema=3.0.1=py36_0
	- krb5=1.16.3=h05b26f9_1001
	- libblas=3.8.0=8_openblas
	- libcblas=3.8.0=8_openblas
	- libcurl=7.64.1=hda55be3_0
	- libedit=3.1.20170329=hf8c457e_1001
	- libffi=3.2.1=he1b5a44_1006
	- libgcc-ng=8.2.0=hdf63c60_1
	- libgfortran-ng=7.3.0=hdf63c60_0
	- libiconv=1.15=h516909a_1005
	- liblapack=3.8.0=8_openblas
	- libpng=1.6.37=hed695b0_0
	- libprotobuf=3.7.1=h8b12597_0
	- libssh2=1.8.2=h22169c7_2
	- libstdcxx-ng=8.2.0=hdf63c60_1
	- libtiff=4.0.10=h648cc4a_1001
	- libtool=2.4.6=h14c3975_1002
	- libuuid=2.32.1=h14c3975_1000
	- libxcb=1.13=h14c3975_1002
	- libxml2=2.9.9=h13577e0_0
	- make=4.2.1=h14c3975_2004
	- markupsafe=1.1.1=py36h14c3975_0
	- multidict=4.5.2=py36h14c3975_1000
	- ncurses=6.1=hf484d3e_1002
	- networkx=2.3=py_0
	- numpy=1.16.3=py36he5ce36f_0
	- openblas=0.3.6=h6e990d7_1
	- openssl=1.1.1b=h14c3975_1
	- pandas=0.24.2=py36hf484d3e_0
	- pandoc=2.7.2=0
	- pango=1.40.14=h4ea9474_1004
	- paramiko=2.4.2=py36_1000
	- pcre=8.41=hf484d3e_1003
	- pip=19.1=py36_0
	- pixman=0.34.0=h14c3975_1003
	- prettytable=0.7.2=py_2
	- protobuf=3.7.1=py36he1b5a44_0
	- psutil=5.6.2=py36h516909a_0
	- pthread-stubs=0.4=h14c3975_1001
	- pyasn1=0.4.4=py_1
	- pyasn1-modules=0.0.5=py36_0
	- pycparser=2.19=py36_1
	- pygraphviz=1.3.1=py36_0
	- pynacl=1.3.0=py36h14c3975_1000
	- pyrsistent=0.15.1=py36h516909a_0
	- pysftp=0.2.9=py36_0
	- python=3.6.7=h381d211_1004
	- python-dateutil=2.8.0=py_0
	- python-irodsclient=0.7.0=py_0
	- pytz=2019.1=py_0
	- pyyaml=5.1=py36h14c3975_0
	- r=3.5.1=r351_1000
	- r-askpass=1.1=r351h96ca727_0
	- r-assertthat=0.2.1=r351h6115d3f_0
	- r-backports=1.1.4=r351hcdcec82_0
	- r-base=3.5.1=h271c98b_1006
	- r-base64enc=0.1_3=r351h96ca727_1002
	- r-bh=1.69.0_1=r351h6115d3f_0
	- r-boot=1.3_22=r351_0
	- r-broom=0.5.2=r351h6115d3f_0
	- r-callr=3.2.0=r351h6115d3f_0
	- r-cellranger=1.1.0=r351h6115d3f_1001
	- r-class=7.3_15=r351h96ca727_1000
	- r-cli=1.1.0=r351h6115d3f_0
	- r-clipr=0.6.0=r351h6115d3f_0
	- r-cluster=2.0.9=r351h9bbef5b_0
	- r-codetools=0.2_16=r351h6115d3f_1000
	- r-colorspace=1.4_1=r351hcdcec82_0
	- r-crayon=1.3.4=r351h6115d3f_1001
	- r-curl=3.3=r351h96ca727_0
	- r-dbi=1.0.0=r351h6115d3f_1001
	- r-dbplyr=1.4.0=r351h6115d3f_0
	- r-digest=0.6.18=r351h96ca727_1000
	- r-dplyr=0.8.0.1=r351h29659fb_1000
	- r-ellipsis=0.1.0=r351h96ca727_0
	- r-evaluate=0.13=r351h6115d3f_1
	- r-fansi=0.4.0=r351h96ca727_1000
	- r-forcats=0.4.0=r351h6115d3f_0
	- r-foreign=0.8_71=r351h96ca727_1002
	- r-fs=1.3.0=r351h0357c0b_0
	- r-generics=0.0.2=r351h6115d3f_1001
	- r-ggplot2=3.1.1=r351h6115d3f_0
	- r-glue=1.3.1=r351hcdcec82_0
	- r-gtable=0.3.0=r351h6115d3f_0
	- r-haven=2.1.0=r351h29659fb_0
	- r-highr=0.8=r351h6115d3f_0
	- r-hms=0.4.2=r351h6115d3f_1000
	- r-htmltools=0.3.6=r351hf484d3e_1002
	- r-httr=1.4.0=r351h6115d3f_1000
	- r-jsonlite=1.6=r351h96ca727_1000
	- r-kernsmooth=2.23_15=r351ha65eedd_1002
	- r-knitr=1.22=r351h6115d3f_0
	- r-labeling=0.3=r351h6115d3f_1001
	- r-lattice=0.20_38=r351h96ca727_1000
	- r-lazyeval=0.2.2=r351hcdcec82_0
	- r-lubridate=1.7.4=r351h29659fb_1001
	- r-magrittr=1.5=r351h6115d3f_1001
	- r-markdown=0.9=r351h96ca727_1000
	- r-mass=7.3_51.4=r351hcdcec82_0
	- r-matrix=1.2_17=r351hcdcec82_0
	- r-mgcv=1.8_28=r351hcdcec82_0
	- r-mime=0.6=r351h96ca727_1000
	- r-modelr=0.1.4=r351h6115d3f_0
	- r-munsell=0.5.0=r351h6115d3f_1001
	- r-nlme=3.1_139=r351h9bbef5b_0
	- r-nnet=7.3_12=r351h96ca727_1002
	- r-openssl=1.3=r351h9c8475f_0
	- r-pillar=1.3.1=r351h6115d3f_1000
	- r-pkgconfig=2.0.2=r351h6115d3f_1001
	- r-plogr=0.2.0=r351h6115d3f_1001
	- r-plyr=1.8.4=r351h29659fb_1002
	- r-prettyunits=1.0.2=r351h6115d3f_1001
	- r-processx=3.3.0=r351hcdcec82_0
	- r-progress=1.2.0=r351h6115d3f_1002
	- r-ps=1.3.0=r351h96ca727_1000
	- r-purrr=0.3.2=r351hcdcec82_0
	- r-r6=2.4.0=r351h6115d3f_0
	- r-rcolorbrewer=1.1_2=r351h6115d3f_1001
	- r-rcpp=1.0.1=r351h0357c0b_0
	- r-readr=1.3.1=r351h29659fb_1000
	- r-readxl=1.3.1=r351h0357c0b_0
	- r-recommended=3.5.1=r351_1001
	- r-rematch=1.0.1=r351h6115d3f_1001
	- r-reprex=0.2.1=r351h6115d3f_1000
	- r-reshape2=1.4.3=r351h29659fb_1003
	- r-rlang=0.3.4=r351hcdcec82_0
	- r-rmarkdown=1.12=r351h6115d3f_0
	- r-rpart=4.1_15=r351hcdcec82_0
	- r-rstudioapi=0.10=r351h6115d3f_0
	- r-rvest=0.3.3=r351h6115d3f_0
	- r-scales=1.0.0=r351h29659fb_1001
	- r-selectr=0.4_1=r351h6115d3f_1000
	- r-spatial=7.3_11=r351h96ca727_1002
	- r-stringi=1.4.3=r351h0357c0b_0
	- r-stringr=1.4.0=r351h6115d3f_0
	- r-survival=2.44_1.1=r351hcdcec82_0
	- r-sys=3.2=r351hcdcec82_0
	- r-tibble=2.1.1=r351hcdcec82_0
	- r-tidyr=0.8.3=r351h0357c0b_0
	- r-tidyselect=0.2.5=r351h29659fb_1000
	- r-tidyverse=1.2.1=r351h6115d3f_1001
	- r-tinytex=0.12=r351h6115d3f_0
	- r-utf8=1.1.4=r351h96ca727_1000
	- r-viridislite=0.3.0=r351h6115d3f_1001
	- r-whisker=0.3_2=r351h6115d3f_1001
	- r-withr=2.1.2=r351h6115d3f_1000
	- r-xfun=0.6=r351h6115d3f_0
	- r-xml2=1.2.0=r351h29659fb_1002
	- r-yaml=2.2.0=r351h96ca727_1001
	- ratelimiter=1.2.0=py36_1000
	- readline=7.0=hf8c457e_1001
	- requests=2.13.0=py36_0
	- rsa=3.1.4=py36_0
	- s3transfer=0.1.13=py36_1001
	- setuptools=41.0.1=py36_0
	- six=1.12.0=py36_1000
	- smmap2=2.0.5=py_0
	- snakemake=5.3.0=2
	- snakemake-minimal=5.3.0=py_2
	- sqlite=3.26.0=h67949de_1001
	- sra-tools=2.9.1_1=h470a237_0
	- tk=8.6.9=h84994c4_1001
	- tktable=2.10=h14c3975_0
	- typing_extensions=3.7.2=py36_1000
	- urllib3=1.12=py36_0
	- wheel=0.33.1=py36_0
	- wrapt=1.11.1=py36h14c3975_0
	- xmlrunner=1.7.7=py_0
	- xorg-kbproto=1.0.7=h14c3975_1002
	- xorg-libice=1.0.9=h516909a_1004
	- xorg-libsm=1.2.3=h84519dc_1000
	- xorg-libx11=1.6.7=h14c3975_1000
	- xorg-libxau=1.0.9=h14c3975_0
	- xorg-libxdmcp=1.1.3=h516909a_0
	- xorg-libxext=1.3.4=h516909a_0
	- xorg-libxpm=3.5.12=h14c3975_1002
	- xorg-libxrender=0.9.10=h516909a_1002
	- xorg-libxt=1.1.5=h14c3975_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
	- yaml=0.1.7=h14c3975_1001
	- yarl=1.3.0=py36h14c3975_1000
	- zlib=1.2.11=h14c3975_1004
	prefix: /home/sovacool/bin/anaconda3/envs/optiFit
	name: test
	channels:
	- conda-forge
	- bioconda
	- defaults
	dependencies:
	- aioeasywebdav=2.2.0=py36_0
	- aiohttp=3.5.4=py36h14c3975_0
	- appdirs=1.4.3=py_1
	- asn1crypto=0.24.0=py36_1003
	- async-timeout=3.0.1=py_1000
	- attrs=19.1.0=py_0
	- bcrypt=3.1.4=py36h470a237_0
	- boto3=1.9.159=py_0
	- botocore=1.12.159=py_0
	- ca-certificates=2019.3.9=hecc5488_0
	- cachetools=2.1.0=py_0
	- cairo=1.16.0=ha4e643d_1000
	- certifi=2019.3.9=py36_0
	- cffi=1.12.3=py36h8022711_0
	- chardet=3.0.4=py36_1003
	- configargparse=0.13.0=py_1
	- cryptography=2.6.1=py36h72c5cf5_0
	- datrie=0.7.1=py36h14c3975_0
	- decorator=4.4.0=py_0
	- docutils=0.14=py36_1001
	- dropbox=9.3.0=py_0
	- expat=2.2.5=hf484d3e_1002
	- filechunkio=1.8=py_2
	- fontconfig=2.13.1=he4413a7_1000
	- freetype=2.10.0=he983fc9_0
	- ftputil=3.4=py_0
	- gettext=0.19.8.1=hc5be6a0_1002
	- gitdb2=2.0.5=py_0
	- gitpython=2.1.11=py_0
	- glib=2.58.3=hf63aee3_1001
	- google-api-core=1.11.0=py36_0
	- google-auth=1.6.3=py_0
	- google-cloud-core=1.0.1=py_0
	- google-cloud-storage=1.16.0=py_0
	- google-resumable-media=0.3.2=py_0
	- googleapis-common-protos=1.6.0=py36_0
	- graphite2=1.3.13=hf484d3e_1000
	- graphviz=2.38.0=hf68f40c_1011
	- harfbuzz=2.4.0=h37c48d4_0
	- icu=58.2=hf484d3e_1000
	- idna=2.8=py36_1000
	- idna_ssl=1.1.0=py36_1000
	- jinja2=2.10.1=py_0
	- jmespath=0.9.4=py_0
	- jpeg=9c=h14c3975_1001
	- jsonschema=3.0.1=py36_0
	- libblas=3.8.0=10_openblas
	- libcblas=3.8.0=10_openblas
	- libffi=3.2.1=he1b5a44_1006
	- libgcc-ng=8.2.0=hdf63c60_1
	- libgfortran-ng=7.3.0=hdf63c60_0
	- libiconv=1.15=h516909a_1005
	- liblapack=3.8.0=10_openblas
	- libpng=1.6.37=hed695b0_0
	- libprotobuf=3.7.1=h8b12597_0
	- libstdcxx-ng=8.2.0=hdf63c60_1
	- libtiff=4.0.10=h57b8799_1003
	- libtool=2.4.6=h14c3975_1002
	- libuuid=2.32.1=h14c3975_1000
	- libxcb=1.13=h14c3975_1002
	- libxml2=2.9.9=h13577e0_0
	- lz4-c=1.8.3=he1b5a44_1001
	- markupsafe=1.1.1=py36h14c3975_0
	- multidict=4.5.2=py36h14c3975_1000
	- ncurses=6.1=hf484d3e_1002
	- networkx=2.3=py_0
	- numpy=1.16.4=py36h95a1406_0
	- openblas=0.3.6=h6e990d7_2
	- openssl=1.1.1b=h14c3975_1
	- pandas=0.24.2=py36hb3f55d8_0
	- pango=1.40.14=h4ea9474_1004
	- paramiko=2.4.2=py36_1000
	- pcre=8.41=hf484d3e_1003
	- pip=19.1=py36_0
	- pixman=0.34.0=h14c3975_1003
	- prettytable=0.7.2=py_2
	- protobuf=3.7.1=py36he1b5a44_0
	- psutil=5.6.2=py36h516909a_0
	- pthread-stubs=0.4=h14c3975_1001
	- pyasn1=0.4.5=py_0
	- pyasn1-modules=0.2.5=py_0
	- pycparser=2.19=py36_1
	- pygraphviz=1.5=py36h14c3975_1000
	- pynacl=1.3.0=py36h14c3975_1000
	- pyopenssl=19.0.0=py36_0
	- pyrsistent=0.15.2=py36h516909a_0
	- pysftp=0.2.9=py_1
	- pysocks=1.7.0=py36_0
	- python=3.6.7=h381d211_1004
	- python-dateutil=2.8.0=py_0
	- python-irodsclient=0.7.0=py_0
	- pytz=2019.1=py_0
	- pyyaml=5.1=py36h14c3975_0
	- ratelimiter=1.2.0=py36_1000
	- readline=7.0=hf8c457e_1001
	- requests=2.22.0=py36_0
	- rsa=3.4.2=py_1
	- s3transfer=0.2.0=py36_0
	- setuptools=41.0.1=py36_0
	- six=1.12.0=py36_1000
	- smmap2=2.0.5=py_0
	- snakemake=5.5.0=0
	- snakemake-minimal=5.5.0=py_0
	- sqlite=3.28.0=h8b20d00_0
	- tk=8.6.9=h84994c4_1001
	- typing_extensions=3.7.2=py36_1000
	- urllib3=1.24.3=py36_0
	- wheel=0.33.4=py36_0
	- wrapt=1.11.1=py36h516909a_0
	- xmlrunner=1.7.7=py_0
	- xorg-kbproto=1.0.7=h14c3975_1002
	- xorg-libice=1.0.9=h516909a_1004
	- xorg-libsm=1.2.3=h84519dc_1000
	- xorg-libx11=1.6.7=h14c3975_1000
	- xorg-libxau=1.0.9=h14c3975_0
	- xorg-libxdmcp=1.1.3=h516909a_0
	- xorg-libxext=1.3.4=h516909a_0
	- xorg-libxpm=3.5.12=h14c3975_1002
	- xorg-libxrender=0.9.10=h516909a_1002
	- xorg-libxt=1.1.5=h14c3975_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
	- yaml=0.1.7=h14c3975_1001
	- yarl=1.3.0=py36h14c3975_1000
	- zlib=1.2.11=h14c3975_1004
	- zstd=1.4.0=h3b9ef0a_0
	prefix: /home/sovacool/bin/anaconda3/envs/test
	#PBS -N smk ## Name of the job for the scheduler
	#PBS -A pschloss_fluxod ## name of the allocation (who is paying for the compute time)
	#PBS -q fluxod ## name of the queue to submit the job to. Will match the suffix on allocation name
	#PBS -l nodes=1:ppn=1,pmem=100MB,walltime=1:00 ## resource reservation max walltime = 672 hours
	#PBS -l qos=flux ## quality of service DO NOT CHANGE THIS
	#PBS -M ## send email notifications to umich email listed
	#PBS -m a ## when to send email a=abort b=job begin e=job end
	#PBS -j oe ## join output & error files to same file, and send to the email listed above
	#PBS -V ## IMPORTANT always use this. send environment setup to node job will be run on
	#
	# Include the next three lines always
	if [ "x${PBS_NODEFILE}" != "x" ] ; then
	cat $PBS_NODEFILE # contains a list of the CPUs you were using if run with PBS
	fi

	# Always add this line to change to the working directory of the program. Otherwise
	# the script will be run from the users /home directory
	cd $PBS_O_WORKDIR
	echo $PBS_O_WORKDIR

	snakemake
	#!/bin/bash

	##################
	#### Slurm preamble

	#### #### #### These are the most frequently changing options

	#### Job name
	#SBATCH --job-name=smk

	#### Request resources here
	#### These are typically, number of processors, amount of memory,
	#### an the amount of time a job requires. May include processor
	#### type, too.

	#SBATCH --nodes=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --cpus-per-task=1
	#SBATCH --mem-per-cpu=200m
	#SBATCH --time=1:00


	#### Slurm account and partition specification here
	#### These will change if you work on multiple projects, or need
	#### special hardware, like large memory nodes or GPUs.

	#SBATCH --account=test
	#SBATCH --partition=standard

	#### #### #### These are the least frequently changing options

	#### Your e-mail address and when you want e-mail

	#SBATCH --mail-user=
	#SBATCH --mail-type=BEGIN,END

	# Add a note here to say what software modules should be loaded.
	# for this job to run successfully.
	# It will be convenient if you give the actual load command(s), e.g.,
	#
	# module load R

	#### End Slurm preamble
	##################


	#### Commands your job should run follow this line

	snakemake

	## If you copied any files to /tmp, make sure you delete them here!