<commit_before># MG-RAST dockerfiles

FROM	debian
MAINTAINER The MG-RAST team

ENV LC_ALL UTF-8
RUN echo 'LC_ALL=UTF-8' >> /etc/environment 
ENV DEBIAN_FRONTEND noninteractive
RUN echo 'DEBIAN_FRONTEND=noninteractive' >> /etc/environment

RUN apt-get update && apt-get install -y \
	bowtie2 	\
	cdbfasta 	\
	cd-hit		\
	dh-autoreconf \
	git 		\
	subversion  \
	jellyfish 	\
	libcwd-guard-perl \
	libberkeleydb-perl \
	libdata-dump-streamer-perl \
	libdatetime-perl \
	libdbi-perl 	\
	libdigest-md5-perl \
	libdigest-md5-file-perl \
	libdbd-pg-perl \
	libemail-simple-perl \
	libemail-sender-perl \
	libfile-slurp-perl \
	libfilehandle-fmode-perl \
	libgetopt-long-descriptive-perl \
	libjson-perl \
	liblist-allutils-perl \
	libpq-dev \
	libpng-dev \
	libposix-strptime-perl \
	libstring-random-perl \
	libtemplate-perl \
	liburi-encode-perl \
	libunicode-escape-perl \
	libwww-perl \
	liblog-log4perl-perl \
	make 		\
	python-biopython \
	python-dev \
	python-leveldb \
	perl-modules \
   	python-numpy \
	python-scipy \
	python-sphinx \
	unzip \
	wget

# ###########
# copy files into image
COPY awecmd/* bin/* /usr/local/bin/
COPY lib/* /usr/local/lib/site_perl/
COPY superblat /usr/local/bin/
RUN chmod 555 /usr/local/bin/* && strip /usr/local/bin/superblat

#### install BLAT from src
RUN cd /root \
	&& wget "http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip" \
	&& unzip blatSrc35.zip && export C_INCLUDE_PATH=/root/include \
	&& export MACHTYPE=x86_64-pc-linux-gnu \
	&& cd blatSrc \
	&& make BINDIR=/usr/local/bin/ \
	&& strip /usr/local/bin/blat \
	&& cd .. \
	&& rm -rf blatSrc blatSrc35.zip

### install FragGeneScan from our patched source in github<commit_msg>locale issue fixed?<commit_after># MG-RAST dockerfiles

FROM	debian
MAINTAINER The MG-RAST team

ENV DEBIAN_FRONTEND noninteractive


RUN apt-get update && apt-get install -y \
	bowtie2 	\
	cdbfasta 	\
	cd-hit		\
	dh-autoreconf \
	git 		\
	subversion  \
	jellyfish 	\
	libcwd-guard-perl \
	libberkeleydb-perl \
	libdata-dump-streamer-perl \
	libdatetime-perl \
	libdbi-perl 	\
	libdigest-md5-perl \
	libdigest-md5-file-perl \
	libdbd-pg-perl \
	libemail-simple-perl \
	libemail-sender-perl \
	libfile-slurp-perl \
	libfilehandle-fmode-perl \
	libgetopt-long-descriptive-perl \
	libjson-perl \
	liblist-allutils-perl \
	libpq-dev \
	libpng-dev \
	libposix-strptime-perl \
	libstring-random-perl \
	libtemplate-perl \
	liburi-encode-perl \
	libunicode-escape-perl \
	libwww-perl \
	liblog-log4perl-perl \
	locales \
	make 		\
	python-biopython \
	python-dev \
	python-leveldb \
	perl-modules \
   	python-numpy \
	python-scipy \
	python-sphinx \
	unzip \
	wget
	

RUN echo 'DEBIAN_FRONTEND=noninteractive' >> /etc/environment
RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales

# ###########
# copy files into image
COPY awecmd/* bin/* /usr/local/bin/
COPY lib/* /usr/local/lib/site_perl/
COPY superblat /usr/local/bin/
RUN chmod 555 /usr/local/bin/* && strip /usr/local/bin/superblat

#### install BLAT from src
RUN cd /root \
	&& wget "http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip" \
	&& unzip blatSrc35.zip && export C_INCLUDE_PATH=/root/include \
	&& export MACHTYPE=x86_64-pc-linux-gnu \
	&& cd blatSrc \
	&& make BINDIR=/usr/local/bin/ \
	&& strip /usr/local/bin/blat \
	&& cd .. \
	&& rm -rf blatSrc blatSrc35.zip

### install FragGeneScan from our patched source in github
{'fraction_non_alphanumeric': 0.13720238095238096, 'fraction_numerical': 0.011011904761904763, 'mean_word_length': 2.9264018691588785, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, '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': '588267', 'n_tokens_mistral': 1497, 'n_tokens_neox': 1369, 'n_words': 248}