Update req

environment.yml

@@ -6,61 +6,81 @@ dependencies:
 - babel=2.3.3=py27_0
 - backports=1.0=py27_0
 - backports.shutil_get_terminal_size=1.0.0=py27_0
+- backports_abc=0.4=py27_0
 - bcftools=1.3=0
 - bedtools=2.25.0=1
 - biopython=1.66=np111py27_0
+- blas=1.1=openblas
 - ca-certificates=2016.2.28=0
-- cairo=1.12.18=6
+- cairo=1.12.18=1
 - click=6.6=py27_0
-- cloog=0.18.0=0
+- cloog=0.18.1=1
 - clyent=1.2.2=py27_0
-- coverage=4.0.3=py27_0
-- curl=7.45.0=1
+- configparser=3.5.0b2=py27_1
+- coverage=3.7.1=py27_0
+- curl=7.49.0=0
 - cycler=0.10.0=py27_0
 - decorator=4.0.9=py27_0
-- docutils=0.12=py27_0
+- docutils=0.12=py27_2
+- entrypoints=0.2.1=py27_0
 - enum34=1.1.6=py27_0
-- expat=2.1.0=0
+- expat=2.1.0=1
 - flake8=2.5.1=py27_0
-- fontconfig=2.11.1=5
-- freetype=2.5.5=0
+- fontconfig=2.11.1=2
+- freetype=2.6.3=0
+- functools32=3.2.3.2=py27_1
 - future=0.15.2=py27_0
 - get_terminal_size=1.0.0=py27_0
 - ghostscript=9.18=0
 - gmp=5.1.2=2
 - htslib=1.3=0
+- icu=56.1=2
 - imagesize=0.7.1=py27_0
+- ipykernel=4.3.1=py27_1
 - ipython=4.2.0=py27_0
 - ipython_genutils=0.1.0=py27_0
+- ipywidgets=5.1.5=py27_0
 - isl=0.12.2=0
-- jinja2=2.8=py27_0
+- jinja2=2.8=py27_1
+- jsonschema=2.5.1=py27_0
+- jupyter_client=4.2.2=py27_0
+- jupyter_core=4.1.0=py27_0
 - lazy-object-proxy=1.2.1=py27_0
 - libgcc=5.2.0=0
 - libgfortran=3.0.0=1
-- libpng=1.6.17=0
+- libiconv=1.14=1
+- libpng=1.6.21=1
+- libsodium=1.0.10=0
 - libxml2=2.9.3=0
 - libxslt=1.1.28=0
 - logilab-common=1.0.2=py27_0
-- markupsafe=0.23=py27_0
-- matplotlib=1.5.1=np111py27_0
+- markupsafe=0.23=py27_2
+- matplotlib=1.5.1=np111py27_1
 - mccabe=0.3.1=py27_0
+- mistune=0.7.2=py27_0
 - mkl=11.3.3=0
-- mpc=1.0.1=0
-- mpfr=3.1.2=0
-- ncurses=5.9=4
-- nose=1.3.7=py27_0
-- numpy=1.11.0=py27_1
-- openblas=0.2.14=0
+- mpc=1.0.3=1
+- mpfr=3.1.4=1
+- nbconvert=4.2.0=py27_0
+- nbformat=4.0.1=py27_0
+- ncurses=5.9=7
+- nose=1.3.7=py27_1
+- notebook=4.2.0=py27_0
+- numpy=1.11.0=py27_blas_openblas_200
+- openblas=0.2.18=1
 - openssl=1.0.2h=0
 - pandas=0.18.1=np111py27_0
 - path.py=8.2.1=py27_0
 - patsy=0.4.1=py27_0
 - pep8=1.7.0=py27_0
-- pexpect=4.0.1=py27_0
-- pickleshare=0.5=py27_0
+- perl=5.22.0=9
+- perl-threaded=5.22.0=10
+- perl-xml-parser=2.44=3
+- pexpect=4.1.0=py27_0
+- pickleshare=0.7.2=py27_0
 - pip=8.1.1=py27_1
 - pixman=0.32.6=0
-- ptyprocess=0.5=py27_0
+- ptyprocess=0.5.1=py27_0
 - py2cairo=1.10.0=py27_2
 - pybedtools=0.7.7=py27_1
 - pybigwig=0.2.8=py27_0
@@ -70,38 +90,53 @@ dependencies:
 - pygments=2.1.3=py27_0
 - pylint=1.5.4=py27_0
 - pymongo=3.0.3=py27_0
-- pyparsing=2.1.1=py27_0
+- pyparsing=2.1.4=py27_0
 - pyqt=4.11.4=py27_1
 - pysam=0.9.0=py27_1
 - python=2.7.11=0
+- python-coveralls=2.5.0=py27_0
 - python-dateutil=2.5.3=py27_0
+- python-pathlib2=2.1.0=py27_0
 - pytz=2016.4=py27_0
 - pyyaml=3.11=py27_1
+- pyzmq=15.2.0=py27_1
 - qt=4.8.7=1
 - readline=6.2=2
 - requests=2.10.0=py27_0
 - samtools=1.3.1=0
-- scipy=0.17.1=np111py27_0
+- scipy=0.17.1=np111py27_blas_openblas_200
 - seaborn=0.7.0=py27_0
-- setuptools=20.7.0=py27_0
+- setuptools=21.2.1=py27_0
+- sh=1.11=py27_0
 - simplegeneric=0.8.1=py27_0
 - singledispatch=3.4.0.3=py27_1
 - sip=4.16.9=py27_0
 - six=1.10.0=py27_0
 - snowballstemmer=1.2.1=py27_0
 - sphinx=1.4.1=py27_0
 - sphinx_rtd_theme=0.1.9=py27_0
-- sqlite=3.9.2=0
-- statsmodels=0.6.1=np111py27_0
+- sqlite=3.13.0=0
+- ssl_match_hostname=3.5.0.1=py27_0
+- statsmodels=0.6.1=np111py27_1
 - system=5.8=2
-- tk=8.5.18=0
+- terminado=0.6=py27_0
+- tk=8.5.19=0
+- tornado=4.3=py27_1
 - traitlets=4.2.1=py27_0
 - wheel=0.29.0=py27_0
+- widgetsnbextension=1.2.3=py27_0
 - wrapt=1.10.6=py27_0
+- xz=5.2.2=0
 - yaml=0.1.6=0
-- zlib=1.2.8=0
+- zeromq=4.1.4=3
+- zlib=1.2.8=3
 - pip:
+  - backports-abc==0.4
   - backports.shutil-get-terminal-size==1.0.0
+  - backports.ssl-match-hostname==3.5.0.1
   - ipython-genutils==0.1.0
+  - jupyter-client==4.2.2
+  - jupyter-core==4.1.0
+  - pathlib2==2.1.0
   - sphinx-rtd-theme==0.1.9
 

requirements.txt

@@ -1,15 +1,22 @@
 alabaster==0.7.7
+anaconda-client==1.4.0
+astroid==1.4.4
 Babel==2.3.3
 backports-abc==0.4
 backports.shutil-get-terminal-size==1.0.0
 backports.ssl-match-hostname==3.5.0.1
 biopython==1.66
+click==6.6
+clyent==1.2.2
 configparser==3.5.0b2
 coverage==3.7.1
 cycler==0.10.0
 decorator==4.0.9
 docutils==0.12
+enum34==1.1.6
+flake8==2.5.1
 functools32==3.2.3.post2
+future==0.15.2
 imagesize==0.7.1
 ipykernel==4.3.1
 ipython==4.2.0
@@ -19,23 +26,32 @@ Jinja2==2.8
 jsonschema==2.5.1
 jupyter-client==4.2.2
 jupyter-core==4.1.0
+lazy-object-proxy==1.2.1
+logilab-common==1.0.2
 MarkupSafe==0.23
 matplotlib==1.5.1
+mccabe==0.3.1
 mistune==0.7.2
 nbconvert==4.2.0
 nbformat==4.0.1
 nose==1.3.7
 notebook==4.2.0
 numpy==1.11.0
 pandas==0.18.1
+path.py==0.0.0
 pathlib2==2.1.0
 patsy==0.4.1
+pep8==1.7.0
 pexpect==4.1.0
 pickleshare==0.7.2
 ptyprocess==0.5.1
 pybedtools==0.7.7
 pyBigWig==0.2.8
+pycairo==1.10.0
+pyfaidx==0.4.7.1
+pyflakes==1.1.0
 Pygments==2.1.3
+pylint==1.5.4
 pymongo==3.0.3
 pyparsing==2.1.4
 pysam==0.9.0
@@ -57,6 +73,6 @@ sphinx-rtd-theme==0.1.9
 statsmodels==0.6.1
 terminado==0.6
 tornado==4.3
-tqdm==4.7.1
 traitlets==4.2.1
 widgetsnbextension==1.2.3
+wrapt==1.10.6