Commit 368d2f70 authored by Marc's avatar Marc
Browse files

add dockerfiles to repository

parent 9c99ece0
FROM ubuntu:18.04
RUN apt-get update && \
apt-get install -y wget && \
apt-get install -y python3 &&\
apt-get install -y ncbi-blast+
ENV INSIDE_CONTAINER=TRUE
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FROM ubuntu:18.04
COPY . /
RUN apt-get update
RUN apt-get -y install perl
RUN apt-get -y install gawk
CMD echo "Container is running"
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FROM ubuntu:18.04
COPY helpers /
RUN apt-get update && \
apt-get install -y wget && \
apt-get install -y python3
RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh
ENV PATH=$PATH:/opt/conda/bin
RUN conda config --add channels r
RUN conda config --add channels bioconda
RUN conda upgrade conda
RUN conda install ghostx && conda update ghostx
ENV PATH=$PATH:/helpers
ENV INSIDE_CONTAINER=TRUE
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#!/usr/bin/python3
import argparse
import fileinput
parser = argparse.ArgumentParser(description='Replaces fasta headers with unique numbers and saves a dictionary of both in tsv format. Caution: The original fasta file gets replaced in the process.')
parser.add_argument('--fasta', '-f', required=True, help='The fasta file')
parser.add_argument('--enum-headers', '-e', required=True, help='File to store enumerated headers in tsv format')
args = parser.parse_args()
fasta = args.fasta
headers_dict = {}
num = 1
with fileinput.FileInput(fasta, inplace=True) as f:
for line in f:
if line.startswith(">"):
header = line.strip().lstrip('>')
headers_dict[num] = header
print(">{}".format(num))
num += 1
else:
print(line, end='')
enum_headers_file = args.enum_headers
with open(enum_headers_file, 'w') as o:
for key in headers_dict:
o.write("{}\t{}\n".format(key, headers_dict[key]))
FROM ubuntu:18.04
RUN apt-get update && \
apt-get install -y python3 && \
apt-get install -y hmmer
ENV INSIDE_CONTAINER=TRUE
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FROM ubuntu:18.04
ADD tools.tar.gz /
RUN apt-get update
RUN apt-get -y install perl
RUN apt-get -y install gawk
RUN apt-get -y install python3
ENV PATH=$PATH:/chlorop-1.1:/signalp-4.1:/targetp-1.1:/tmhmm-2.0c/bin:/helpers
ENV INSIDE_CONTAINER=TRUE
#!/usr/bin/python3
import argparse
import fileinput
parser = argparse.ArgumentParser(description='Replaces fasta headers with unique numbers and saves a dictionary of both in tsv format. Caution: The original fasta file gets replaced in the process.')
parser.add_argument('--fasta', '-f', required=True, help='The fasta file')
parser.add_argument('--enum-headers', '-e', required=True, help='File to store enumerated headers in tsv format')
args = parser.parse_args()
fasta = args.fasta
headers_dict = {}
num = 1
with fileinput.FileInput(fasta, inplace=True) as f:
for line in f:
if line.startswith(">"):
header = line.strip().lstrip('>')
headers_dict[num] = header
print(">{}".format(num))
num += 1
else:
print(line, end='')
enum_headers_file = args.enum_headers
with open(enum_headers_file, 'w') as o:
for key in headers_dict:
o.write("{}\t{}\n".format(key, headers_dict[key]))
FROM ubuntu:18.04
COPY . /
RUN apt-get update && apt-get -y install perl
CMD echo "Container is running"
\ No newline at end of file
FROM ubuntu:18.04
COPY . /
RUN apt-get update
RUN apt-get -y install perl
RUN apt-get -y install gawk
CMD echo "Container is running"
\ No newline at end of file
FROM ubuntu:18.04
COPY . /
RUN apt-get update && apt-get -y install perl
CMD echo "Container is running"
\ No newline at end of file
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