helenebioinf / bat Goto Github PK
View Code? Open in Web Editor NEWBAT - Bisulfite Analyss Toolkit
License: MIT License
BAT - Bisulfite Analyss Toolkit
License: MIT License
Does it interest you to have a conda recipe available for BAT? At our institution, users are not able to run docker commands, but users can manage a conda distribution in their network drives. I have an environment.yml file that installs most of the requirements for BAT via bioconda (https://bioconda.github.io/), it might not be too much more work to build a conda recipe that includes all of the dependencies and allows for a simple install of BAT via bioconda.
# environment.yml
name: BAT
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- bedtools=2.27.1=he941832_2
- circos=0.69.6=3
- cutadapt=1.18=py36_0
- fastqc=0.11.8=0
- htslib=1.9=hc238db4_4
- libdeflate=1.0=h470a237_0
- metilene=0.2.6=h470a237_1
- perl-app-cpanminus=1.7044=pl526_1
- perl-autoloader=5.74=pl526_1
- perl-carp=1.38=pl526_1
- perl-clone=0.41=pl526h470a237_0
- perl-config-general=2.61=pl526_1
- perl-constant=1.33=pl526_1
- perl-data-dumper=2.161=pl526_2
- perl-digest-perl-md5=1.9=pl526_1
- perl-dynaloader=1.25=pl526_1
- perl-encode=2.88=pl526_1
- perl-exporter=5.72=pl526_1
- perl-exporter-tiny=1.000000=pl526_0
- perl-extutils-makemaker=7.34=pl526_2
- perl-file-copy-link=0.140=pl526h470a237_1
- perl-file-path=2.15=pl526_0
- perl-file-spec=3.48_01=pl526_1
- perl-file-temp=0.2304=pl526_2
- perl-font-ttf=1.06=pl526_0
- perl-gd=2.69=pl526he941832_0
- perl-getopt-long=2.50=pl526_1
- perl-io-string=1.08=pl526_3
- perl-list-moreutils=0.428=pl526_1
- perl-list-moreutils-xs=0.428=pl526_0
- perl-list-util=1.38=pl526_1
- perl-math-bezier=0.01=pl526_1
- perl-math-round=0.07=pl526_1
- perl-math-vecstat=0.08=pl526_1
- perl-module-implementation=0.09=pl526_2
- perl-module-runtime=0.016=pl526_0
- perl-number-format=1.75=pl526_3
- perl-params-validate=1.29=pl526h470a237_0
- perl-parent=0.236=pl526_1
- perl-pathtools=3.73=h470a237_2
- perl-readonly=1.04=pl526_2
- perl-regexp-common=2017060201=pl526_0
- perl-scalar-list-utils=1.45=pl526h470a237_3
- perl-set-intspan=1.19=pl526_1
- perl-statistics-basic=1.6611=pl526_2
- perl-svg=2.84=pl526_0
- perl-test-more=1.001002=pl526_1
- perl-text-format=0.59=pl526_1
- perl-time-hires=1.9758=pl526_0
- perl-try-tiny=0.30=pl526_0
- perl-xml-parser=2.44=pl526h3a4f0e9_6
- perl-xsloader=0.24=pl526_0
- samtools=1.9=h8ee4bcc_1
- segemehl=0.3.1=haeeaa98_0
- xopen=0.3.5=py_0
- bz2file=0.98=py_0
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.10.15=ha4d7672_0
- cairo=1.14.12=h276e583_5
- certifi=2018.10.15=py36_1000
- curl=7.61.0=h93b3f91_2
- expat=2.2.5=hfc679d8_2
- fontconfig=2.13.1=h65d0f4c_0
- freetype=2.9.1=h6debe1e_4
- gettext=0.19.8.1=h5e8e0c9_1
- giflib=5.1.4=h470a237_1
- glib=2.56.2=h464dc38_1
- gmp=6.1.2=hfc679d8_0
- graphite2=1.3.12=hfc679d8_1
- harfbuzz=1.9.0=h04dbb29_1
- icu=58.2=hfc679d8_0
- jpeg=9c=h470a237_1
- krb5=1.14.6=0
- libedit=3.1.20170329=haf1bffa_1
- libffi=3.2.1=hfc679d8_5
- libgcc-ng=7.2.0=hdf63c60_3
- libgd=2.2.5=h5400f36_4
- libgfortran=3.0.0=1
- libiconv=1.15=h470a237_3
- libpng=1.6.35=ha92aebf_2
- libssh2=1.8.0=h5b517e9_3
- libstdcxx-ng=7.2.0=hdf63c60_3
- libtiff=4.0.9=he6b73bb_2
- libuuid=2.32.1=h470a237_2
- libwebp=0.5.2=7
- libxcb=1.13=h470a237_2
- libxml2=2.9.8=h422b904_5
- mpfr=4.0.1=h16a7912_0
- ncurses=6.1=hfc679d8_1
- openjdk=11.0.1=h470a237_2
- openjpeg=2.3.0=h0e734dc_3
- openssl=1.0.2p=h470a237_1
- pango=1.40.14=he752989_2
- pcre=8.41=hfc679d8_3
- perl=5.26.2=h470a237_0
- pigz=2.3.4=0
- pip=18.1=py36_1000
- pixman=0.34.0=h470a237_3
- poppler=0.67.0=hdf8a1b3_2
- poppler-data=0.4.9=0
- pthread-stubs=0.4=h470a237_1
- python=3.6.7=h5001a0f_1
- r-assertthat=0.2.0=r351h6115d3f_1001
- r-base=3.5.1=h4fe35fd_1
- r-bitops=1.0_6=r351hc070d10_2
- r-catools=1.17.1.1=r351h9d2a408_2
- r-cli=1.0.0=r351h6115d3f_1001
- r-colorspace=1.3_2=r351hc070d10_2
- r-crayon=1.3.4=r351h6115d3f_1001
- r-digest=0.6.18=r351hc070d10_0
- r-fansi=0.3.0=r351hc070d10_0
- r-gdata=2.18.0=r351h6115d3f_1001
- r-getopt=1.20.2=r351_2001
- r-ggplot2=3.1.0=r351h6115d3f_1000
- r-glue=1.3.0=r351h470a237_2
- r-gplots=3.0.1=r351h6115d3f_1001
- r-gtable=0.2.0=r351h6115d3f_1001
- r-gtools=3.8.1=r351hc070d10_2
- r-kernsmooth=2.23_15=r351h364d78e_2
- r-labeling=0.3=r351h6115d3f_1001
- r-lattice=0.20_35=r351hc070d10_0
- r-lazyeval=0.2.1=r351hc070d10_2
- r-magrittr=1.5=r351h6115d3f_1001
- r-mass=7.3_50=r351hc070d10_2
- r-matrix=1.2_14=r351hc070d10_2
- r-mgcv=1.8_24=r351hc070d10_2
- r-munsell=0.5.0=r351h6115d3f_1001
- r-nlme=3.1_137=r351h364d78e_0
- r-optparse=1.6.0=r351_1001
- r-pillar=1.3.0=r351h6115d3f_1000
- r-plyr=1.8.4=r351h9d2a408_2
- r-r6=2.2.2=r351h6115d3f_1001
- r-rcolorbrewer=1.1_2=r351h6115d3f_1001
- r-rcpp=1.0.0=r351h9d2a408_0
- r-reshape2=1.4.3=r351h9d2a408_2
- r-rlang=0.3.0.1=r351h470a237_0
- r-scales=1.0.0=r351h9d2a408_1
- r-stringi=1.2.4=r351h9d2a408_1
- r-stringr=1.3.1=r351h6115d3f_1001
- r-tibble=1.4.2=r351hc070d10_2
- r-utf8=1.1.4=r351hc070d10_0
- r-viridislite=0.3.0=r351h6115d3f_1001
- r-withr=2.1.2=r351h6115d3f_1000
- readline=7.0=haf1bffa_1
- setuptools=40.6.2=py36_0
- six=1.11.0=py36_1001
- sqlite=3.25.3=hb1c47c0_0
- tectonic=0.1.11=h99d305b_0
- tk=8.6.9=ha92aebf_0
- wheel=0.32.3=py36_0
- xorg-kbproto=1.0.7=h470a237_2
- xorg-libice=1.0.9=h470a237_4
- xorg-libsm=1.2.3=h8c8a85c_0
- xorg-libx11=1.6.6=h470a237_0
- xorg-libxau=1.0.8=h470a237_6
- xorg-libxdmcp=1.1.2=h470a237_7
- xorg-libxext=1.3.3=h470a237_4
- xorg-libxrender=0.9.10=h470a237_2
- xorg-libxt=1.1.5=h470a237_2
- xorg-renderproto=0.11.1=h470a237_2
- xorg-xextproto=7.3.0=h470a237_2
- xorg-xproto=7.0.31=h470a237_7
- xz=5.2.4=h470a237_1
- zlib=1.2.11=h470a237_3
- gsl=2.2.1=h0c605f7_3
- libcurl=7.61.0=h1ad7b7a_0
- pip:
- absl-py==0.2.2
- argcomplete==1.9.4
- argh==0.26.2
- bcbio-gff==0.6.4
- geojson==2.4.0
- grpcio==1.13.0
- ipyvolume==0.4.5
- ipywebrtc==0.3.0
- jupyter-contrib-nbextensions==0.5.0
- jupyter-latex-envs==1.4.4
- jupyter-nbextensions-configurator==0.4.0
- markdown==2.6.11
- sklearn==0.0
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.