<commit_before>FROM kbase/kbase:sdkbase.latest
MAINTAINER KBase Developer
# -----------------------------------------

# Insert apt-get instructions here to install
# any required dependencies for your module.

# RUN apt-get update
RUN pip install coverage
RUN pip install dropbox
RUN pip install requests --upgrade \
    && pip install 'requests[security]' --upgrade \
    && ( [ $(pip show filemagic|grep -c filemagic) -eq 0 ] || pip uninstall -y filemagic ) \
    && pip install python-magic

# Get NCBI SRATools (for fastq-dump)
RUN cd /kb/dev_container/modules && \
    mkdir NCBI_SRA_tools && cd NCBI_SRA_tools && \
    curl 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz' -O && \
    tar zxf sratoolkit.2.8.2-ubuntu64.tar.gz && \
    cp sratoolkit.2.8.2-ubuntu64/bin/fastq-dump.2.8.2  /kb/deployment/bin/fastq-dump
# -----------------------------------------

COPY ./ /kb/module
RUN mkdir -p /kb/module/work
RUN chmod -R 777 /kb/module

WORKDIR /kb/module

RUN make all

ENTRYPOINT [ "./scripts/entrypoint.sh" ]
<commit_msg>update Dockerfile<commit_after>FROM kbase/kbase:sdkbase.latest
MAINTAINER KBase Developer
# -----------------------------------------

# Insert apt-get instructions here to install
# any required dependencies for your module.

# RUN apt-get update
RUN pip install coverage
RUN pip install dropbox
RUN pip install requests --upgrade \
    && pip install 'requests[security]' --upgrade \
    && ( [ $(pip show filemagic|grep -c filemagic) -eq 0 ] || pip uninstall -y filemagic ) \
    && pip install python-magic

# Get NCBI SRATools (for fastq-dump)
RUN cd /kb/dev_container/modules && \
    mkdir NCBI_SRA_tools && cd NCBI_SRA_tools && \
    curl 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz' -O && \
    tar zxf sratoolkit.2.8.2-ubuntu64.tar.gz && \
    cp sratoolkit.2.8.2-ubuntu64/bin/fastq-dump.2.8.2  /kb/deployment/bin/fastq-dump
# -----------------------------------------

COPY ./ /kb/module
RUN mkdir -p /kb/module/work
RUN chmod -R a+rw /kb/module

WORKDIR /kb/module

RUN make all

ENTRYPOINT [ "./scripts/entrypoint.sh" ]

{'fraction_non_alphanumeric': 0.19962599345488546, 'fraction_numerical': 0.021972884525479196, 'mean_word_length': 2.3229813664596275, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5055538', 'n_tokens_mistral': 779, 'n_tokens_neox': 714, 'n_words': 181}