Conda environment

General
1

How can I create a conda environment in a docker container??

2

Hi :slight_smile:

Is this what you’re looking for?
https://hub.docker.com/r/continuumio/miniconda/

3

Something like that but i have a set of dependencies in a file that i want to install in a docker container.

4

what kind of dependencies?

The miniconda image is based on debian, so you could just apt-get those dependencies?

5

dependencies:

  • R::r=3.3.1=r3.3.1_0

  • R::r-base=3.3.1=5

  • R::r-boot=1.3_18=r3.3.1_0

  • R::r-class=7.3_14=r3.3.1_0

  • R::r-cluster=2.0.4=r3.3.1_0

  • R::r-codetools=0.2_14=r3.3.1_0

  • R::r-foreign=0.8_66=r3.3.1_0

  • R::r-kernsmooth=2.23_15=r3.3.1_0

  • R::r-lattice=0.20_33=r3.3.1_0

  • R::r-mass=7.3_45=r3.3.1_0

  • R::r-matrix=1.2_6=r3.3.1_0

  • R::r-mgcv=1.8_12=r3.3.1_0

  • R::r-nlme=3.1_128=r3.3.1_0

  • R::r-nnet=7.3_12=r3.3.1_0

  • R::r-recommended=3.3.1=r3.3.1_0

  • R::r-rpart=4.1_10=r3.3.1_0

  • R::r-spatial=7.3_11=r3.3.1_0

  • R::r-survival=2.39_4=r3.3.1_0

  • backports=1.0=py27_0

  • bioconda::bcftools=1.3.1=0

  • bioconda::curl=7.45.0=1

  • bioconda::ghostscript=9.18=0

  • bioconda::gimmemotifs=0.10.0b4=py27pl5.22.0_1

  • bioconda::htslib=1.3.1=1

  • bioconda::kid=0.9.6=py27_1

  • bioconda::lightning=0.2.dev0=py27_0

  • bioconda::meme=4.11.1=py27pl5.22.0_1

  • bioconda::moods=1.9.0=py27_0

  • bioconda::perl=5.22.0=9

  • bioconda::perl-digest-hmac=1.03=0

  • bioconda::perl-encode-locale=1.05=3

  • bioconda::perl-file-listing=6.04=0

  • bioconda::perl-html-parser=3.72=0

  • bioconda::perl-html-tagset=3.20=0

  • bioconda::perl-http-cookies=6.01=0

  • bioconda::perl-http-daemon=6.01=0

  • bioconda::perl-http-date=6.02=0

  • bioconda::perl-http-message=6.11=0

  • bioconda::perl-http-negotiate=6.01=0

  • bioconda::perl-io-html=1.001=0

  • bioconda::perl-io-socket-ssl=2.024=0

  • bioconda::perl-libwww-perl=6.15=0

  • bioconda::perl-lwp-mediatypes=6.02=0

  • bioconda::perl-net-http=6.09=0

  • bioconda::perl-net-ssleay=1.74=0

  • bioconda::perl-ntlm=1.09=1

  • bioconda::perl-threaded=5.22.0=10

  • bioconda::perl-uri=1.71=0

  • bioconda::perl-www-robotrules=6.02=0

  • bioconda::perl-xml-parser=2.44=4

  • bioconda::pybedtools=0.7.8=py27_1

  • bioconda::pysam=0.9.1=py27_1

  • bioconda::r-robustrankaggreg=1.1=r3.3.1_0

  • bioconda::samtools=1.3.1=4

  • bioconda::ucsc-genepredtobed=332=0

  • bzip2=1.0.6=3

  • cairo=1.12.18=6

  • cloog=0.18.0=0

  • cycler=0.10.0=py27_0

  • dbus=1.10.10=0

  • decorator=4.0.10=py27_0

  • django=1.8.2=py27_0

  • enum34=1.1.6=py27_0

  • expat=2.1.0=0

  • fontconfig=2.11.1=6

  • freetype=2.5.5=1

  • gcc=4.8.5=6

  • get_terminal_size=1.0.0=py27_0

  • glib=2.43.0=1

  • gmp=5.1.2=2

  • gsl=2.2.1=0

  • gst-plugins-base=1.8.0=0

  • gstreamer=1.8.0=0

  • harfbuzz=0.9.39=1

  • icu=54.1=0

  • ipython=5.1.0=py27_0

  • ipython_genutils=0.1.0=py27_0

  • isl=0.12.2=0

  • jbig=2.1=0

  • jinja2=2.8=py27_1

  • jpeg=8d=1

  • lcms=1.19=0

  • libffi=3.2.1=0

  • libgcc=5.2.0=0

  • libgfortran=3.0.0=1

  • libpng=1.6.22=0

  • libtiff=4.0.6=2

  • libxcb=1.12=0

  • libxml2=2.9.2=0

  • libxslt=1.1.28=0

  • markupsafe=0.23=py27_2

  • matplotlib=1.5.3=np111py27_0

  • mkl=11.3.3=0

  • mpc=1.0.1=0

  • mpfr=3.1.2=0

  • mysql=5.5.24=0

  • mysql-python=1.2.5=py27_0

  • ncurses=5.9=8

  • numpy=1.11.1=py27_0

  • openssl=1.0.2i=0

  • pandas=0.18.1=np111py27_0

  • pango=1.39.0=1

  • path.py=8.2.1=py27_0

  • pathlib2=2.1.0=py27_0

  • patsy=0.4.1=py27_0

  • pcre=8.39=1

  • pexpect=4.0.1=py27_0

  • pickleshare=0.7.4=py27_0

  • pil=1.1.7=py27_2

  • pip=8.1.2=py27_0

  • pixman=0.32.6=0

  • prompt_toolkit=1.0.3=py27_0

  • ptyprocess=0.5.1=py27_0

  • pycairo=1.10.0=py27_0

  • pygments=2.1.3=py27_0

  • pymc=2.3.6=np111py27_2

  • pyparsing=2.1.4=py27_0

  • pyqt=5.6.0=py27_0

  • python=2.7.12=1

  • python-dateutil=2.5.3=py27_0

  • pytz=2016.6.1=py27_0

  • pyyaml=3.12=py27_0

  • qt=5.6.0=0

  • readline=6.2=2

  • scikit-learn=0.18=np111py27_0

  • scipy=0.18.1=np111py27_0

  • seaborn=0.7.1=py27_0

  • setuptools=27.2.0=py27_0

  • simplegeneric=0.8.1=py27_1

  • sip=4.18=py27_0

  • six=1.10.0=py27_0

  • sqlite=3.13.0=0

  • statsmodels=0.6.1=np111py27_1

  • tk=8.5.18=0

  • traitlets=4.3.0=py27_0

  • wcwidth=0.1.7=py27_0

  • wheel=0.29.0=py27_0

  • xz=5.2.2=0

  • yaml=0.1.6=0

  • zlib=1.2.8=3

6

Thats the whole list of dependencies that i want to install and most of them cant be installed using pip. Sorry for such a long list

7

I dont know conda, but if needs pip, you can install python, and then pip install the requirements.

8

thank you but i tried pip it didnt work

9

Hie Martin. The miniconda image pretty well but its so big. Thanks very much.