Notebook that details the different docker images, how to get them, what their purpose is and what software packages come default. Also gives examples on how to get new packages.
Based on the Debian Jessie (will likely move to alpine) linux image. Software packages installed are centered around taking sequence reads and processing them using any of the well established software packages (bowtie2, bwa, RSEM, Origami, HiCPro, etc) into commonly accepted output formats, such as FPKM, differential expression, normalized interactions, etc.
Based on the Debian Jessie (moving to alpine) linux image. Includes machine learning PyTorch ready to go. It can train and test the Convolutional Neural Network (CNN) + Long Short Term Memory (LSTM). Its loaded with the ability to call Insulated Neighborhoods using a louvian algorithm and then annotate each chromatin accessibility peak falling within them. The identities of each TF are estimated using the trained neural network. Eventually it outputs JSON files storing the annotated INs
Based on the minimal Alpine Linux image (starts at 4.5Mb!). On top are only the packages required in order to run plotly and jupyter in order to give a simple front end to the annotated insulated neighborhoods. Use this if you want to visualize the Insulated Neighborhood graphs.
The pipelines available and their capabilities are described in Methods which helps you pick the right of 3 Docker images.
Remember to define the correct directories when running the Docker image depending on your local OS machine, ex:
Whitehead (Linux):
-v "/lab/solexa_public:/input_dir" \
-v "/home/dborgesr/work_space/tmp:/tmp_dir" \
-v "/home/dborgesr/work_space/out_dir:/output_dir" \
-v "/home/dborgesr/work_space/annotation:/annotation_dir" \docker run --name megatid -p 8891:8891 -tid \
-v "/your/input/directory:/input_dir" \
-v "/your/temporary/directory/:/tmp_dir" \
-v "/your/output/directory/:/output_dir" \
-v "/your/annotation/directory/:/annotation_dir" \
dborgesr/euplotid:megatiddocker run --name euplotid -p 8890:8890 -tid \
-v "/your/input/directory:/input_dir" \
-v "/your/temporary/directory/:/tmp_dir" \
-v "/your/output/directory/:/output_dir" \
-v "/your/annotation/directory/:/annotation_dir" \
dborgesr/euplotid:euplotiddocker run --name minitid -p 8892:8892 -tid \
-v "/your/input/directory:/input_dir" \
-v "/your/temporary/directory/:/tmp_dir" \
-v "/your/output/directory/:/output_dir" \
-v "/your/annotation/directory/:/annotation_dir" \
dborgesr/euplotid:minitiddocker run --name nanotid -p 8893:8893 -tid \
-v "/your/input/directory:/input_dir" \
-v "/your/temporary/directory/:/tmp_dir" \
-v "/your/output/directory/:/output_dir" \
-v "/your/annotation/directory/:/annotation_dir" \
dborgesr/euplotid:nanotidEach Docker image has different capabilities (packages installed in each Docker image are described in packageManagement)
In [2]:
!docker pull dborgesr/euplotid:megatid
!docker pull dborgesr/euplotid:euplotid
!docker pull dborgesr/euplotid:minitid
In [9]:
#Megatid
docker run --name megatid_cont -p 8891:8891 -tid \
-v "/lab/solexa_public/:/input_dir" \
-v "/home/dborgesr/work_space/tmp/:/tmp_dir" \
-v "/home/dborgesr/work_space/out_dir/:/output_dir" \
-v "/home/dborgesr/work_space/annotation:/annotation_dir" \
dborgesr/euplotid:megatid
#Euplotid
docker run --name euplotid_cont -p 8890:8890 -tid \
-v "/lab/solexa_public/:/input_dir" \
-v "/home/dborgesr/work_space/tmp/:/tmp_dir" \
-v "/home/dborgesr/work_space/out_dir/:/output_dir" \
-v "/home/dborgesr/work_space/annotation:/annotation_dir" \
dborgesr/euplotid:euplotid
#Minitid
docker run --name minitid_cont -p 8892:8892 -tid \
-v "/lab/solexa_public/:/input_dir" \
-v "/home/dborgesr/work_space/tmp/:/tmp_dir" \
-v "/home/dborgesr/work_space/out_dir/:/output_dir" \
-v "/home/dborgesr/work_space/annotation:/annotation_dir" \
dborgesr/euplotid:minitid
In [ ]:
!docker stop $(docker ps -a -q)
!docker rm $(docker ps -a -q)
!docker rmi $(docker images -a -q)
In [1]:
!cd /root/Euplotid/ && git pull
Conda is an AWESOME software package handler and I use it to upkeep all these images, here is a useful cheat sheet! Conda can easily add many many packages and handles all the version handling and dirty backend. Also allows us to easily export our environment for full and fast replicability.
In [ ]:
#List all packages on current machine using conda
!conda list
In [10]:
#export settings which include all packages to a file which you can share to be loaded anywhere
!conda env export --name root > /tmp/cur_enviro.yaml
In [ ]:
#Install new package and specify channel and version
!conda install -c bioconda samtools=1.4.1
| Megatid | Euplotid | Minitid |
|---|---|---|
| _license=1.1 | _license=1.1 | _nb_ext_conf=0.3.0 |
| _nb_ext_conf=0.3.0 | _nb_ext_conf=0.3.0 | anaconda-client=1.6.3 |
| alabaster=0.7.10 | alabaster=0.7.9 | asn1crypto=0.22.0 |
| anaconda=custom | anaconda=4.2.0 | bcftools=1.4.1 |
| anaconda-clean=1.1.0 | anaconda-clean=1.0.0 | bedops=2.4.26 |
| anaconda-client=1.6.3 | anaconda-client=1.5.1 | biopython=1.68 |
| anaconda-navigator=1.5.2 | anaconda-navigator=1.3.1 | bleach=1.5.0 |
| anaconda-project=0.6.0 | argcomplete=1.0.0 | bzip2=1.0.6 |
| argcomplete=1.8.2 | argparse=1.4.0 | cffi=1.10.0 |
| asn1crypto=0.22.0 | astroid=1.4.7 | clyent=1.2.2 |
| astroid=1.4.8 | astropy=1.2.1 | conda=4.3.18 |
| astropy=1.3.2 | babel=2.3.4 | conda-env=2.6.0 |
| autoconf=2.69 | backports=1.0 | cryptography=1.8.1 |
| babel=2.3.4 | backports_abc=0.4 | curl=7.52.1 |
| backports=1.0 | beautifulsoup4=4.5.1 | dbus=1.10.10 |
| bamtools=2.4.0 | biopython=1.69 | decorator=4.0.11 |
| bash_kernel=0.6 | bitarray=0.8.1 | entrypoints=0.2.2 |
| beautifulsoup4=4.5.3 | blaze=0.10.1 | expat=2.1.0 |
| bedops=2.4.26 | bokeh=0.12.2 | fontconfig=2.12.1 |
| bedtools=2.26.0 | boto=2.42.0 | freetype=2.5.5 |
| bitarray=0.8.1 | bottleneck=1.1.0 | git=2.11.1 |
| blas=1.1 | bx-python=0.7.3 | glib=2.50.2 |
| blat=35 | cairo=1.12.18 | gst-plugins-base=1.8.0 |
| blaze=0.10.1 | cdecimal=2.3 | gstreamer=1.8.0 |
| bleach=1.4.2 | cffi=1.7.0 | html5lib=0.999 |
| bokeh=0.12.5 | chest=0.2.3 | htslib=1.4.1 |
| boto=2.46.1 | click=6.6 | icu=54.1 |
| boto3=1.4.4 | cloudpickle=0.2.1 | idna=2.5 |
| botocore=1.5.39 | clyent=1.2.2 | ipykernel=4.6.1 |
| bottleneck=1.2.0 | colorama=0.3.7 | ipython=6.0.0 |
| bowtie=1.2.0 | conda=4.2.9 | ipython_genutils=0.2.0 |
| bowtie2=2.3.2 | conda-build=2.0.2 | ipywidgets=6.0.0 |
| bwa=0.7.15 | configobj=5.0.6 | jbig=2.1 |
| bzip2=1.0.6 | configparser=3.5.0 | jedi=0.10.2 |
| ca-certificates=2017.4.17 | contextlib2=0.5.3 | jinja2=2.9.6 |
| cairo=1.14.6 | cryptography=1.5 | joblib=0.11 |
| certifi=2017.4.17 | curl=7.49.0 | jpeg=9b |
| cffi=1.10.0 | cycler=0.10.0 | jsonschema=2.6.0 |
| chardet=3.0.2 | cython=0.24.1 | jupyter=1.0.0 |
| chest=0.2.3 | cytoolz=0.8.0 | jupyter_client=5.0.1 |
| click=6.7 | dask=0.11.0 | jupyter_console=5.1.0 |
| cloog=0.18.0 | datashape=0.5.2 | jupyter_core=4.3.0 |
| cloudpickle=0.2.2 | dbus=1.10.10 | libffi=3.2.1 |
| clyent=1.2.1 | decorator=4.0.10 | libgcc=5.2.0 |
| colorama=0.3.9 | dill=0.2.5 | libgfortran=3.0.0 |
| conda=4.2.13 | docutils=0.12 | libiconv=1.14 |
| conda-build=2.1.10 | dynd-python=0.7.2 | libpng=1.6.27 |
| conda-env=2.6.0 | entrypoints=0.2.2 | libsodium=1.0.10 |
| conda-verify=2.0.0 | enum34=1.1.6 | libtiff=4.0.6 |
| configobj=5.0.6 | et_xmlfile=1.0.1 | libxcb=1.12 |
| contextlib2=0.5.5 | expat=2.1.0 | libxml2=2.9.4 |
| cryptography=1.8.1 | fastcache=1.0.2 | markupsafe=0.23 |
| curl=7.52.1 | filelock=2.0.6 | mistune=0.7.4 |
| cycler=0.10.0 | flask=0.11.1 | mkl=2017.0.1 |
| cython=0.25.2 | flask-cors=2.1.2 | mmtf-python=1.0.5 |
| cytoolz=0.8.2 | fontconfig=2.11.1 | msgpack-python=0.4.8 |
| dask=0.14.3 | freetype=2.5.5 | mygene=2.3.0 |
| datashape=0.5.4 | funcsigs=1.0.2 | myvariant=0.3.1 |
| dbus=1.10.10 | functools32=3.2.3.2 | nb_anacondacloud=1.2.0 |
| decorator=4.0.11 | futures=3.0.5 | nb_conda=2.0.0 |
| dill=0.2.6 | get_terminal_size=1.0.0 | nb_conda_kernels=2.0.0 |
| distributed=1.16.3 | gevent=1.1.2 | nbconvert=5.1.1 |
| docutils=0.13.1 | Ghost.py=0.2.3 | nbformat=4.3.0 |
| dynd-python=0.7.2 | glib=2.43.0 | nbpresent=3.0.2 |
| entrypoints=0.2.2 | greenlet=0.4.10 | networkx=1.11 |
| et_xmlfile=1.0.1 | grin=1.2.1 | notebook=5.0.0 |
| expat=2.1.0 | gst-plugins-base=1.8.0 | numpy=1.12.1 |
| fastcache=1.0.2 | gstreamer=1.8.0 | olefile=0.44 |
| fastqc=0.11.5 | h5py=2.6.0 | openssl=1.0.2k |
| filelock=2.0.6 | harfbuzz=0.9.39 | packaging=16.8 |
| flask=0.12 | hdf5=1.8.17 | pandas=0.20.1 |
| flask-cors=3.0.2 | heapdict=1.0.0 | pandocfilters=1.4.1 |
| fontconfig=2.12.1 | html5lib=0.999999999 | path.py=10.3.1 |
| fortran-magic=0.7 | icu=54.1 | pcre=8.39 |
| freetype=2.7 | idna=2.1 | pexpect=4.2.1 |
| gcc=4.8.5 | imagesize=0.7.1 | pickleshare=0.7.4 |
| get_terminal_size=1.0.0 | ipaddress=1.0.16 | pillow=4.1.1 |
| gettext=0.19.7 | ipykernel=4.5.0 | pip=9.0.1 |
| gevent=1.1rc4 | ipython=5.1.0 | plotly=1.12.9 |
| ghostscript=9.18 | ipython_genutils=0.1.0 | prompt_toolkit=1.0.14 |
| giflib=5.1.4 | ipywidgets=5.2.2 | ptyprocess=0.5.1 |
| git=2.12.2 | itsdangerous=0.24 | pycosat=0.6.2 |
| glib=2.51.4 | jbig=2.1 | pycparser=2.17 |
| gmp=6.1.2 | jdcal=1.2 | pycrypto=2.6.1 |
| graphite2=1.3.9 | jedi=0.9.0 | pygments=2.2.0 |
| graphviz=2.38.0 | jinja2=2.8 | pyliftover=0.3 |
| greenlet=0.4.12 | joblib=0.11 | pyopenssl=17.0.0 |
| gsl=2.2.1 | jpeg=8d | pyparsing=2.1.4 |
| gst-plugins-base=1.8.0 | jsonschema=2.5.1 | pyqt=5.6.0 |
| gstreamer=1.8.0 | jupyter=1.0.0 | pysam=0.11.2.1 |
| h5py=2.7.0 | jupyter_client=4.4.0 | python=3.5.3 |
| harfbuzz=1.4.3 | jupyter_console=5.0.0 | python-dateutil=2.6.0 |
| hdf5=1.8.17 | jupyter_core=4.2.0 | pytorch=0.1.12 |
| heapdict=1.0.0 | lazy-object-proxy=1.2.1 | pytz=2017.2 |
| homer=4.8.3 | libdynd=0.7.2 | pyyaml=3.12 |
| html5lib=0.999999999 | libffi=3.2.1 | pyzmq=16.0.2 |
| htslib=1.4.1 | libgcc=4.8.5 | qt=5.6.2 |
| icu=58.1 | libgfortran=3.0.0 | qtconsole=4.3.0 |
| idna=2.5 | libpng=1.6.22 | readline=6.2 |
| imageio=2.1.2 | libsodium=1.0.10 | reportlab=3.4.0 |
| imagesize=0.7.1 | libtiff=4.0.6 | requests=2.14.2 |
| ipykernel=4.6.1 | libxcb=1.12 | ruamel_yaml=0.11.14 |
| ipyparallel=6.0.2 | libxml2=2.9.2 | samtools=1.4.1 |
| ipython=6.0.0 | libxslt=1.1.28 | scipy=0.19.0 |
| ipython_genutils=0.2.0 | llvmlite=0.13.0 | setuptools=27.2.0 |
| ipywidgets=6.0.0 | locket=0.2.0 | simplegeneric=0.8.1 |
| isl=0.12.2 | lxml=3.6.4 | sip=4.18 |
| isort=4.2.5 | MACS2=2.1.1.20160309 | six=1.10.0 |
| itsdangerous=0.24 | markupsafe=0.23 | sqlite=3.13.0 |
| java-jdk=8.0.92 | matplotlib=1.5.3 | terminado=0.6 |
| jbig=2.1 | mechanize=0.3.3 | testpath=0.3 |
| jdcal=1.3 | mistune=0.7.3 | tk=8.5.18 |
| jedi=0.10.0 | mkl=11.3.3 | torchvision=0.1.8 |
| jinja2=2.9.5 | mkl-service=1.1.2 | tornado=4.5.1 |
| jmespath=0.9.0 | mpmath=0.19 | traitlets=4.3.2 |
| jpeg=9b | multipledispatch=0.4.8 | wcwidth=0.1.7 |
| jsonschema=2.5.1 | mygene=3.0.0 | wheel=0.29.0 |
| jupyter=1.0.0 | myvariant=0.3.1 | widgetsnbextension=2.0.0 |
| jupyter-c-kernel=1.0.0 | nb_anacondacloud=1.2.0 | xz=5.2.2 |
| jupyter_client=5.0.1 | nb_conda=2.0.0 | yaml=0.1.6 |
| jupyter_console=5.1.0 | nb_conda_kernels=2.0.0 | zeromq=4.1.5 |
| jupyter_core=4.3.0 | nbbrowserpdf=0.2.0 | zlib=1.2.8 |
| lazy-object-proxy=1.3.0 | nbconvert=4.2.0 | |
| libdynd=0.7.2 | nbformat=4.1.0 | |
| libffi=3.2.1 | nbformat=4.3.0 | |
| libgcc=5.2.0 | nbpresent=3.0.2 | |
| libgd=2.2.4 | networkx=1.11 | |
| libgfortran=3.0.0 | nltk=3.2.1 | |
| libiconv=1.14 | nose=1.3.7 | |
| libmagic=5.25 | notebook=4.2.3 | |
| libpng=1.6.28 | numba=0.28.1 | |
| libsodium=1.0.10 | numexpr=2.6.1 | |
| libtiff=4.0.6 | numpy=1.11.1 | |
| libwebp=0.5.2 | odo=0.5.0 | |
| libxcb=1.12 | openpyxl=2.3.2 | |
| libxml2=2.9.4 | openssl=1.0.2j | |
| libxslt=1.1.29 | pandas=0.18.1 | |
| llvmlite=0.18.0 | partd=0.3.6 | |
| locket=0.2.0 | patchelf=0.9 | |
| lxml=3.7.3 | path.py=8.2.1 | |
| lzo=2.06 | pathlib2=2.1.0 | |
| m4=1.4.17 | patsy=0.4.1 | |
| make=4.2.1 | pdfrw=0.3 | |
| markupsafe=0.23 | pep8=1.7.0 | |
| matplotlib=2.0.2 | pexpect=4.0.1 | |
| mccabe=0.6.1 | pickleshare=0.7.4 | |
| mistune=0.7.4 | pillow=3.3.1 | |
| mkl=2017.0.1 | pip=9.0.1 | |
| mkl-service=1.1.2 | pip=8.1.2 | |
| mpc=1.0.3 | pixman=0.32.6 | |
| mpfr=3.1.5 | pkginfo=1.3.2 | |
| mpmath=0.19 | plotly=2.0.8 | |
| msgpack-python=0.4.8 | ply=3.9 | |
| multipledispatch=0.4.9 | prompt_toolkit=1.0.3 | |
| nb_anacondacloud=1.4.0 | psutil=4.3.1 | |
| nb_conda=2.2.0 | ptyprocess=0.5.1 | |
| nb_conda_kernels=2.1.0 | py=1.4.31 | |
| nbconvert=5.1.1 | pyasn1=0.1.9 | |
| nbformat=4.3.0 | pycairo=1.10.0 | |
| nbpresent=3.0.2 | pycosat=0.6.1 | |
| ncurses=5.9 | pycparser=2.14 | |
| networkx=1.11 | pycrypto=2.6.1 | |
| nltk=3.2.2 | pycurl=7.43.0 | |
| nose=1.3.7 | pyflakes=1.3.0 | |
| notebook=5.0.0 | pygments=2.1.3 | |
| numba=0.33.0 | pyliftover=0.3 | |
| numexpr=2.6.2 | pylint=1.5.4 | |
| numpy=1.12.1 | pyopenssl=16.0.0 | |
| numpydoc=0.6.0 | pyparsing=2.1.4 | |
| odo=0.5.0 | PyPDF2=1.26.0 | |
| olefile=0.44 | pyqt=5.6.0 | |
| openblas=0.2.19 | pysam=0.11.2.1 | |
| openjdk=8.0.121 | pytables=3.2.3.1 | |
| openpyxl=2.4.0 | pytest=2.9.2 | |
| openssl=1.0.2k | python=2.7.12 | |
| packaging=16.8 | python-dateutil=2.5.3 | |
| pandas=0.20.1 | python-louvain=0.6 | |
| pandoc=1.19.2 | pytz=2016.6.1 | |
| pandocfilters=1.4.1 | pyyaml=3.12 | |
| pango=1.40.4 | pyzmq=15.4.0 | |
| partd=0.3.8 | qt=5.6.0 | |
| patchelf=0.9 | qtawesome=0.3.3 | |
| path.py=8.2.1 | qtconsole=4.2.1 | |
| pathlib2=2.2.1 | qtpy=1.1.2 | |
| patsy=0.4.1 | readline=6.2 | |
| pcre=8.39 | redis=3.2.0 | |
| pep8=1.7.0 | redis-py=2.10.5 | |
| perl=5.22.0.1 | reportlab=3.4.0 | |
| perl-aceperl=1.92 | requests=2.11.1 | |
| perl-algorithm-munkres=0.08 | rope=0.9.4 | |
| perl-app-cpanminus=1.7039 | rst2pdf-0.93.dev=r0 | |
| perl-appconfig=1.71 | ruamel_yaml=0.11.14 | |
| perl-array-compare=2.11 | scikit-image=0.12.3 | |
| perl-bio-asn1-entrezgene=1.72 | scikit-learn=0.17.1 | |
| perl-bio-featureio=1.6.905 | scipy=0.18.1 | |
| perl-bio-phylo=0.58 | seaborn=0.7.1 | |
| perl-bio-samtools=1.43 | setuptools=27.2.0 | |
| perl-bioperl=1.6.924 | simplegeneric=0.8.1 | |
| perl-bioperl-core=1.6.924 | singledispatch=3.4.0.3 | |
| perl-bioperl-run=1.006900 | sip=4.18 | |
| perl-cgi=4.22 | six=1.10.0 | |
| perl-class-inspector=1.28 | snowballstemmer=1.2.1 | |
| perl-class-method-modifiers=2.11 | sockjs-tornado=1.0.3 | |
| perl-clone=0.38 | sphinx=1.4.6 | |
| perl-common-sense=3.74 | spyder=3.0.0 | |
| perl-convert-binary-c=0.78 | sqlalchemy=1.0.13 | |
| perl-convert-binhex=1.125 | sqlite=3.13.0 | |
| perl-crypt-rc4=2.02 | ssl_match_hostname=3.4.0.2 | |
| perl-data-stag=0.14 | statsmodels=0.6.1 | |
| perl-dbd-sqlite=1.50 | sympy=1.0 | |
| perl-dbi=1.636 | terminado=0.6 | |
| perl-devel-globaldestruction=0.13 | tk=8.5.18 | |
| perl-digest-hmac=1.03 | toolz=0.8.0 | |
| perl-digest-perl-md5=1.9 | tornado=4.4.1 | |
| perl-email-date-format=1.005 | traitlets=4.3.0 | |
| perl-encode-locale=1.05 | unicodecsv=0.14.1 | |
| perl-error=0.17024 | uuid=1.30 | |
| perl-exporter-tiny=0.042 | Wand=0.4.4 | |
| perl-file-listing=6.04 | wcwidth=0.1.7 | |
| perl-file-slurp-tiny=0.004 | webencodings=0.5.1 | |
| perl-file-sort=1.01 | weblogo=3.5.0 | |
| perl-file-which=1.20 | werkzeug=0.11.11 | |
| perl-font-afm=1.20 | wheel=0.29.0 | |
| perl-gd=2.56 | widgetsnbextension=1.2.6 | |
| perl-graph=0.9704 | wrapt=1.10.6 | |
| perl-graphviz=2.20 | xlrd=1.0.0 | |
| perl-html-element-extended=1.18 | xlsxwriter=0.9.3 | |
| perl-html-entities-numbered=0.04 | xlwt=1.1.2 | |
| perl-html-formatter=2.14 | xz=5.2.2 | |
| perl-html-parser=3.72 | yaml=0.1.6 | |
| perl-html-tableextract=2.13 | zeromq=4.1.4 | |
| perl-html-tagset=3.20 | zlib=1.2.8 | |
| perl-html-tidy=1.56 | ||
| perl-html-tree=5.03 | ||
| perl-html-treebuilder-xpath=0.14 | ||
| perl-http-cookies=6.01 | ||
| perl-http-daemon=6.01 | ||
| perl-http-date=6.02 | ||
| perl-http-message=6.11 | ||
| perl-http-negotiate=6.01 | ||
| perl-image-info=1.38 | ||
| perl-image-size=3.300 | ||
| perl-io-html=1.001 | ||
| perl-io-sessiondata=1.03 | ||
| perl-io-socket-ssl=2.024 | ||
| perl-io-string=1.08 | ||
| perl-io-stringy=2.111 | ||
| perl-io-tty=1.12 | ||
| perl-ipc-run=0.94 | ||
| perl-jcode=2.07 | ||
| perl-json=2.90 | ||
| perl-json-xs=2.34 | ||
| perl-libwww-perl=6.15 | ||
| perl-libxml-perl=0.08 | ||
| perl-list-moreutils=0.413 | ||
| perl-lwp-mediatypes=6.02 | ||
| perl-lwp-protocol-https=6.06 | ||
| perl-lwp-simple=6.15 | ||
| perl-mailtools=2.14 | ||
| perl-math-cdf=0.1 | ||
| perl-math-derivative=0.04 | ||
| perl-math-random=0.72 | ||
| perl-math-spline=0.02 | ||
| perl-mime-lite=3.030 | ||
| perl-mime-tools=5.507 | ||
| perl-mime-types=2.12 | ||
| perl-mldbm=2.05 | ||
| perl-module-runtime=0.014 | ||
| perl-moo=2.001000 | ||
| perl-net-http=6.09 | ||
| perl-net-ssleay=1.74 | ||
| perl-ntlm=1.09 | ||
| perl-ole-storage_lite=0.19 | ||
| perl-parse-recdescent=1.967013 | ||
| perl-pdf-api2=2.025 | ||
| perl-postscript=0.06 | ||
| perl-role-tiny=2.000001 | ||
| perl-set-scalar=1.29 | ||
| perl-soap-lite=1.19 | ||
| perl-sort-naturally=1.03 | ||
| perl-spreadsheet-parseexcel=0.65 | ||
| perl-spreadsheet-writeexcel=2.40 | ||
| perl-statistics-descriptive=3.0612 | ||
| perl-sub-exporter-progressive=0.001011 | ||
| perl-svg=2.64 | ||
| perl-svg-graph=0.02 | ||
| perl-task-weaken=1.04 | ||
| perl-template-toolkit=2.26 | ||
| perl-test-leaktrace=0.15 | ||
| perl-test-pod=1.51 | ||
| perl-threaded=5.22.0 | ||
| perl-tie-ixhash=1.23 | ||
| perl-timedate=2.30 | ||
| perl-tree-dag_node=1.29 | ||
| perl-type-tiny=1.000005 | ||
| perl-unicode-map=0.112 | ||
| perl-uri=1.71 | ||
| perl-www-robotrules=6.02 | ||
| perl-xml-dom=1.45 | ||
| perl-xml-dom-xpath=0.14 | ||
| perl-xml-filter-buffertext=1.01 | ||
| perl-xml-libxml=2.0124 | ||
| perl-xml-libxslt=1.94 | ||
| perl-xml-namespacesupport=1.11 | ||
| perl-xml-parser=2.44 | ||
| perl-xml-regexp=0.04 | ||
| perl-xml-sax=0.99 | ||
| perl-xml-sax-base=1.08 | ||
| perl-xml-sax-expat=0.51 | ||
| perl-xml-sax-writer=0.56 | ||
| perl-xml-simple=2.22 | ||
| perl-xml-twig=3.49 | ||
| perl-xml-writer=0.625 | ||
| perl-xml-xpath=1.33 | ||
| perl-xml-xpathengine=0.14 | ||
| perl-yaml=1.18 | ||
| pexpect=4.2.1 | ||
| pickleshare=0.7.3 | ||
| pillow=4.1.1 | ||
| pip=9.0.1 | ||
| pixman=0.34.0 | ||
| pkginfo=1.2.1 | ||
| plotly=2.0.7 | ||
| ply=3.9 | ||
| prompt_toolkit=1.0.14 | ||
| psutil=5.2.1 | ||
| ptyprocess=0.5.1 | ||
| py=1.4.33 | ||
| pyasn1=0.2.3 | ||
| pycosat=0.6.1 | ||
| pycparser=2.17 | ||
| pycrypto=2.6.1 | ||
| pycurl=7.43.0 | ||
| pyflakes=1.5.0 | ||
| pygments=2.2.0 | ||
| pylint=1.6.5 | ||
| pyopenssl=16.2.0 | ||
| pyparsing=2.2.0 | ||
| pyqt=5.6.0 | ||
| pytables=3.4.2 | ||
| pytest=3.0.7 | ||
| python=3.5.3 | ||
| python-dateutil=2.6.0 | ||
| pytz=2017.2 | ||
| pywavelets=0.5.2 | ||
| pyyaml=3.12 | ||
| pyzmq=16.0.2 | ||
| qt=5.6.2 | ||
| qtawesome=0.4.4 | ||
| qtconsole=4.3.0 | ||
| qtpy=1.2.1 | ||
| r-assertthat=0.1 | ||
| r-backports=1.0.4 | ||
| r-base=3.3.2 | ||
| r-base64enc=0.1_3 | ||
| r-bh=1.62.0_1 | ||
| r-bitops=1.0_6 | ||
| r-boot=1.3_18 | ||
| r-broom=0.4.1 | ||
| r-car=2.1_4 | ||
| r-caret=6.0_73 | ||
| r-catools=1.17.1 | ||
| r-class=7.3_14 | ||
| r-cluster=2.0.5 | ||
| r-codetools=0.2_15 | ||
| r-colorspace=1.3_1 | ||
| r-crayon=1.3.2 | ||
| r-curl=2.3 | ||
| r-data.table=1.10.0 | ||
| r-dbi=0.5_1 | ||
| r-dichromat=2.0_0 | ||
| r-digest=0.6.10 | ||
| r-dplyr=0.5.0 | ||
| r-essentials=1.5.2 | ||
| r-evaluate=0.10 | ||
| r-forcats=0.1.1 | ||
| r-foreach=1.4.3 | ||
| r-foreign=0.8_67 | ||
| r-formatr=1.4 | ||
| r-ggplot2=2.2.0 | ||
| r-gistr=0.3.6 | ||
| r-glmnet=2.0_5 | ||
| r-gtable=0.2.0 | ||
| r-haven=1.0.0 | ||
| r-hexbin=1.27.1 | ||
| r-highr=0.6 | ||
| r-hms=0.3 | ||
| r-htmltools=0.3.5 | ||
| r-htmlwidgets=0.8 | ||
| r-httpuv=1.3.3 | ||
| r-httr=1.2.1 | ||
| r-irdisplay=0.4.4 | ||
| r-irkernel=0.7.1 | ||
| r-iterators=1.0.8 | ||
| r-jsonlite=1.1 | ||
| r-kernsmooth=2.23_15 | ||
| r-knitr=1.15.1 | ||
| r-labeling=0.3 | ||
| r-lattice=0.20_34 | ||
| r-lazyeval=0.2.0 | ||
| r-lme4=1.1_12 | ||
| r-lubridate=1.6.0 | ||
| r-magrittr=1.5 | ||
| r-maps=3.1.1 | ||
| r-markdown=0.7.7 | ||
| r-mass=7.3_45 | ||
| r-matrix=1.2_7.1 | ||
| r-matrixmodels=0.4_1 | ||
| r-mgcv=1.8_16 | ||
| r-mime=0.5 | ||
| r-minqa=1.2.4 | ||
| r-mnormt=1.5_5 | ||
| r-modelmetrics=1.1.0 | ||
| r-modelr=0.1.0 | ||
| r-munsell=0.4.3 | ||
| r-nlme=3.1_128 | ||
| r-nloptr=1.0.4 | ||
| r-nnet=7.3_12 | ||
| r-openssl=0.9.5 | ||
| r-pbdzmq=0.2_4 | ||
| r-pbkrtest=0.4_6 | ||
| r-plyr=1.8.4 | ||
| r-pryr=0.1.2 | ||
| r-psych=1.6.9 | ||
| r-purrr=0.2.2 | ||
| r-quantmod=0.4_7 | ||
| r-quantreg=5.29 | ||
| r-r6=2.2.0 | ||
| r-randomforest=4.6_12 | ||
| r-rbokeh=0.5.0 | ||
| r-rcolorbrewer=1.1_2 | ||
| r-rcpp=0.12.8 | ||
| r-rcppeigen=0.3.2.9.0 | ||
| r-readr=1.0.0 | ||
| r-readxl=0.1.1 | ||
| r-recommended=3.3.2 | ||
| r-repr=0.10 | ||
| r-reshape2=1.4.2 | ||
| r-rmarkdown=1.3 | ||
| r-rpart=4.1_10 | ||
| r-rprojroot=1.1 | ||
| r-rvest=0.3.2 | ||
| r-scales=0.4.1 | ||
| r-selectr=0.3_0 | ||
| r-shiny=0.14.2 | ||
| r-sourcetools=0.1.5 | ||
| r-sparsem=1.74 | ||
| r-spatial=7.3_11 | ||
| r-stringi=1.1.2 | ||
| r-stringr=1.1.0 | ||
| r-survival=2.40_1 | ||
| r-tibble=1.2 | ||
| r-tidyr=0.6.0 | ||
| r-tidyverse=1.0.0 | ||
| r-ttr=0.23_1 | ||
| r-uuid=0.1_2 | ||
| r-xml2=1.0.0 | ||
| r-xtable=1.8_2 | ||
| r-xts=0.9_7 | ||
| r-yaml=2.1.14 | ||
| r-zoo=1.7_13 | ||
| readline=6.2 | ||
| redis=3.2.0 | ||
| redis-py=2.10.5 | ||
| requests=2.13.0 | ||
| rope=0.10.5 | ||
| ruamel_yaml=0.11.14 | ||
| s3fs=0.1.0 | ||
| s3transfer=0.1.10 | ||
| samtools=1.4.1 | ||
| scikit-image=0.13.0 | ||
| scikit-learn=0.18.1 | ||
| scipy=0.19.0 | ||
| seaborn=0.7.1 | ||
| setuptools=33.1.1 | ||
| sickle=0.5 | ||
| simplegeneric=0.8.1 | ||
| singledispatch=3.4.0.3 | ||
| sip=4.18 | ||
| six=1.10.0 | ||
| snowballstemmer=1.2.1 | ||
| sockjs-tornado=1.0.3 | ||
| sortedcontainers=1.5.3 | ||
| sphinx=1.6.1 | ||
| sphinxcontrib-websupport=1.0.1 | ||
| spyder=3.1.4 | ||
| sqlalchemy=1.1.5 | ||
| sqlite=3.13.0 | ||
| sra-tools=2.8.1 | ||
| star=2.5.3a | ||
| statsmodels=0.8.0 | ||
| sympy=1.0 | ||
| tbb=4.4_20150728 | ||
| tblib=1.3.2 | ||
| terminado=0.6 | ||
| testpath=0.3 | ||
| tidyp=1.04 | ||
| tk=8.5.19 | ||
| toolz=0.8.2 | ||
| tornado=4.5.1 | ||
| traitlets=4.3.2 | ||
| trimmomatic=0.36 | ||
| typing=3.5.2.2 | ||
| unicodecsv=0.14.1 | ||
| wcwidth=0.1.7 | ||
| webencodings=0.5 | ||
| weblogo=2.8.2 | ||
| werkzeug=0.11.10 | ||
| wheel=0.29.0 | ||
| widgetsnbextension=2.0.0 | ||
| wkhtmltopdf=0.12.3 | ||
| wrapt=1.10.8 | ||
| xlrd=1.0.0 | ||
| xlsxwriter=0.9.6 | ||
| xlwt=1.2.0 | ||
| xorg-libxau=1.0.8 | ||
| xorg-libxdmcp=1.1.2 | ||
| xz=5.2.2 | ||
| yaml=0.1.6 | ||
| zeromq=4.1.5 | ||
| zict=0.1.2 | ||
| zlib=1.2.8 |