<commit_before>FROM ubuntu:14.04

MAINTAINER <NAME> <EMAIL>

#install make
RUN apt-get -qq install make

#Install clustalw modeled on http://www.microhowto.info/howto/perform_an_unattended_installation_of_a_debian_package.html
RUN echo "deb http://archive.ubuntu.com/ubuntu trusty multiverse" >> /etc/apt/sources.list
RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y clustalw

#install cpan minus modeled from http://perlmaven.com/install-perl-modules-without-root-rights-on-linux-ubuntu-13-10
RUN apt-get -qq install curl && curl -L http://cpanmin.us | perl - App::cpanminus

# Install BioPerl Run Package modeled from genomicpariscentre/bioperl:latest
RUN cpanm --force CJFIELDS/BioPerl-Run-1.006900.tar.gz

#Install Log4perl modeled on https://hub.docker.com/r/sjackman/assemblers/~/dockerfile/
RUN cpanm Log::Log4perl

#ncbi-blast modeled from https://bcrc.bio.umass.edu/courses/spring2012/micbio/micbio660/content/blast
RUN apt-get -qq install blast2

#Get AAARFv.1.0.1.pl code and add into $PATH to make it executable anywhere, then make it executable
ADD https://github.com/jdebarry/AAARF/raw/master/v1.0.1/AAARFv1.0.1.pl /usr/bin/
RUN [ "chmod", "+x",  "/usr/bin/AAARFv1.0.1.pl" ]

#create directory for running
CMD mkdir data

#Running AAARF - Input file and BLASTdb files must be in same folder and this folder must be used as input folder for command line execution of image
#Command Line Usage of Image: docker run --rm -v=/path/to/host/input/folder:/data AAARF --inputFile=/data/InputFileName
ENTRYPOINT ["AAARFv1.0.1.pl"]
<commit_msg>Updating Run Instructions in DockerFile<commit_after>FROM ubuntu:14.04

MAINTAINER <NAME> <EMAIL>

#install make
RUN apt-get -qq install make

#Install clustalw modeled on http://www.microhowto.info/howto/perform_an_unattended_installation_of_a_debian_package.html
RUN echo "deb http://archive.ubuntu.com/ubuntu trusty multiverse" >> /etc/apt/sources.list
RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y clustalw

#install cpan minus modeled from http://perlmaven.com/install-perl-modules-without-root-rights-on-linux-ubuntu-13-10
RUN apt-get -qq install curl && curl -L http://cpanmin.us | perl - App::cpanminus

# Install BioPerl Run Package modeled from genomicpariscentre/bioperl:latest
RUN cpanm --force CJFIELDS/BioPerl-Run-1.006900.tar.gz

#Install Log4perl modeled on https://hub.docker.com/r/sjackman/assemblers/~/dockerfile/
RUN cpanm Log::Log4perl

#ncbi-blast modeled from https://bcrc.bio.umass.edu/courses/spring2012/micbio/micbio660/content/blast
RUN apt-get -qq install blast2

#Get AAARFv.1.0.1.pl code and add into $PATH to make it executable anywhere, then make it executable
ADD https://github.com/jdebarry/AAARF/raw/master/v1.0.1/AAARFv1.0.1.pl /usr/bin/
RUN [ "chmod", "+x",  "/usr/bin/AAARFv1.0.1.pl" ]

#create directory for running
CMD mkdir data

#Running AAARF - Input file and BLASTdb files must be in same folder and this folder must be used as input folder for command line execution of image
#Command Line Usage of Image: docker run --rm -v=/path/to/host/input/folder:/data jdebarry/aaarf --inputFile=/data/InputFileName
ENTRYPOINT ["AAARFv1.0.1.pl"]

{'fraction_non_alphanumeric': 0.11313315134971186, 'fraction_numerical': 0.024264482863208977, 'mean_word_length': 4.552188552188552, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 11, 'https://': 6, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3036391', 'n_tokens_mistral': 1256, 'n_tokens_neox': 1147, 'n_words': 304}