Commit afdff62b authored by Zdralovic Edim's avatar Zdralovic Edim

changed directories to shared storage

parents 7dbf69ce 8983dd79
......@@ -2,15 +2,15 @@ FROM python:2.7
ENV LANG C.UTF-8
LABEL MAINTAINER "edim.zdralovic@unibas.ch"
#Installing Singularity
ENV SINGU_VERSION 2.5.0
#Installing Singularity(provided by Nina)
ENV SINGU_VERSION 2.5.1
WORKDIR /home
RUN apt-get -y update
RUN apt-get install --yes python python-pip build-essential wget \
squashfs-tools git-all nodejs\
&& pip install html5lib \
&& pip install libarchive \
&& wget https://github.com/singularityware/singularity/releases/download/$SINGU_VERSION/singularity-$SINGU_VERSION.tar.gz \
RUN apt-get install --yes libarchive-dev --yes python python-pip build-essential wget \
squashfs-tools git-all nodejs \
&& pip install html5lib
RUN wget https://github.com/singularityware/singularity/releases/download/$SINGU_VERSION/singularity-$SINGU_VERSION.tar.gz \
&& tar xvf singularity-$SINGU_VERSION.tar.gz \
&& cd singularity-$SINGU_VERSION \
&& ./configure --prefix=/usr/local \
......@@ -19,16 +19,6 @@ RUN apt-get install --yes python python-pip build-essential wget \
#Installing Toil
WORKDIR /home
#RUN git clone https://github.com/common-workflow-language/cwltool.git \
# && cd cwltool \
# && pip2 install . \
# && CWL_VERSION=$(cwltool --version | cut -d' ' -f 2 | cut -d'.' -f 3) \
# && cd .. \
# && git clone https://github.com/BD2KGenomics/toil.git \
# && cd toil \
# Replace toil's default cwltool version with current one
# && sed -ri "s/cwltool==1\.0\.[0-9]{14}/cwltool==1\.0\.$CWL_VERSION/" setup.py \
# && pip install .[cwl]
RUN git clone --branch 3.15.0 https://github.com/BD2KGenomics/toil.git \
&& cd toil \
&& pip2 install .[cwl] \
......
FROM python:2.7
ENV LANG C.UTF-8
LABEL MAINTAINER "edim.zdralovic@unibas.ch"
#Installing Singularity(provided by Nina)
ENV SINGU_VERSION 2.4.2
WORKDIR /home
RUN apt-get -y update
RUN apt-get install --yes python python-pip build-essential wget \
squashfs-tools git-all nodejs\
&& pip install html5lib \
&& wget https://github.com/singularityware/singularity/releases/download/$SINGU_VERSION/singularity-$SINGU_VERSION.tar.gz \
&& tar xvf singularity-$SINGU_VERSION.tar.gz \
&& cd singularity-$SINGU_VERSION \
&& ./configure --prefix=/usr/local \
&& make \
&& make install
#Installing Toil
WORKDIR /home
RUN git clone https://github.com/common-workflow-language/cwltool.git \
&& cd cwltool \
&& git checkout -b 1.0.20180518123035 \
&& pip2 install . \
&& CWL_VERSION=$(cwltool --version | cut -d' ' -f 2 | cut -d'.' -f 3) \
&& cd .. \
&& git clone https://github.com/BD2KGenomics/toil.git \
&& cd toil \
&& git checkout -b f7cfd7f73a284b28e3618beac117df77a28a857c \
# Replace toil's default cwltool version with current one
&& sed -ri "s/cwltool==1\.0\.[0-9]{14}/cwltool==1\.0\.$CWL_VERSION/" setup.py \
&& pip install .[cwl]
#Installing Python 3
RUN apt-get -y install build-essential checkinstall \
&& apt-get -y install libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev \
&& wget https://www.python.org/ftp/python/3.6.0/Python-3.6.0.tar.xz \
&& tar xvf Python-3.6.0.tar.xz \
&& cd Python-3.6.0/ \
&& ./configure \
&& make altinstall \
&& apt-get install sqlite3
COPY Flask/ /krinicwl/
COPY requirements.txt /krinicwl/
WORKDIR /krinicwl/
RUN pip3.6 install -r requirements.txt
WORKDIR /krinicwl/cwlREST
CMD ["python3.6", "cwlRESTService.py"]
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