<commit_before>
## see https://www.digitalocean.com/community/tutorials/docker-explained-using-dockerfiles-to-automate-building-of-images
## https://docs.docker.com/articles/dockerfile_best-practices/

## see https://registry.hub.docker.com/u/rocker/shiny/dockerfile/
FROM ubuntu

RUN apt-get install -y git

## force image rebuild after changing sources by changing comment in line
RUN mkdir /tissue_miner && git clone https://github.com/mpicbg-scicomp/tissue_miner /tissue_miner/ ## test2

## http://stackoverflow.com/questions/20635472/using-the-run-instruction-in-a-dockerfile-with-source-does-not-work
RUN /bin/bash -c "source /tissue_miner/misc/install_dependencies.sh"

#RUN ${TM_HOME}/tissue_miner/Setup.R | tee tm_setup.log

## compile the parser needed to convert TissueAnalyzer outputs into csv
#RUN cd ${TM_HOME}/parser && make clean && make<commit_msg>added bash profile to Dockerfile<commit_after>
## see https://www.digitalocean.com/community/tutorials/docker-explained-using-dockerfiles-to-automate-building-of-images
## https://docs.docker.com/articles/dockerfile_best-practices/

## see https://registry.hub.docker.com/u/rocker/shiny/dockerfile/
FROM ubuntu

RUN apt-get install -y git

## force image rebuild after changing sources by changing comment in line
RUN mkdir /tissue_miner && git clone https://github.com/mpicbg-scicomp/tissue_miner /tissue_miner/ ## test3

## http://stackoverflow.com/questions/20635472/using-the-run-instruction-in-a-dockerfile-with-source-does-not-work
RUN /bin/bash -c "source /tissue_miner/misc/install_dependencies.sh"

#RUN ${TM_HOME}/tissue_miner/Setup.R | tee tm_setup.log

## compile the parser needed to convert TissueAnalyzer outputs into csv
#RUN cd ${TM_HOME}/parser && make clean && make

## also add bash profile
COPY docker_bash_profile.sh /.bash_profile
{'fraction_non_alphanumeric': 0.12596259625962597, 'fraction_numerical': 0.009900990099009901, 'mean_word_length': 4.84887459807074, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 8, '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': '5647714', 'n_tokens_mistral': 652, 'n_tokens_neox': 592, 'n_words': 126}