add dockerfiles to repository

docker/blastp_swissprot/Dockerfile

+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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docker/chlorop/Dockerfile

+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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docker/ghostx_swissprot/Dockerfile

+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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docker/ghostx_swissprot/helpers/reduce_fasta_headers_to_enumeration.py

+#!/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]))

docker/hmmer_pfam_a/Dockerfile

+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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docker/psot/Dockerfile

+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
+

docker/psot/helpers/reduce_fasta_headers_to_enumeration.py

+#!/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]))

docker/signalp/Dockerfile

+FROM ubuntu:18.04
+
+COPY . /
+
+RUN apt-get update && apt-get -y install perl
+
+CMD echo "Container is running"
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docker/targetp/Dockerfile

+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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docker/thhmm/Dockerfile

+FROM ubuntu:18.04
+
+COPY . /
+
+RUN apt-get update && apt-get -y install perl
+
+CMD echo "Container is running"
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