khanlab/cfmm2tar:v0.0.1f

$ singularity pull shub://khanlab/cfmm2tar:v0.0.1f

Singularity Recipe

Bootstrap: docker
From: ubuntu:xenial
#########

%setup
#########
mkdir -p $SINGULARITY_ROOTFS/src
cp *.sh  $SINGULARITY_ROOTFS/src

mkdir -p $SINGULARITY_ROOTFS/apps/cfmm2tar
cp *.py  $SINGULARITY_ROOTFS/apps/cfmm2tar
cp cfmm2tar $SINGULARITY_ROOTFS/apps/cfmm2tar

#########
%post
#########

#needed for keytool
if [ ! -e /dev/fd ]
then
ln -s /proc/self/fd /dev/fd
fi

export DEBIAN_FRONTEND=noninteractive
apt-get update && apt-get install -y --no-install-recommends apt-utils \
    sudo \
    git \
    wget \
    curl \
    zip \
    unzip \
    python2.7 \
    python-pip \
    rsync \
    openssh-client

sudo pip install --upgrade pip
sudo pip install --upgrade setuptools

#for some unknown reason, need change the mode:
chmod a+x /apps/cfmm2tar/*.py


##install pydicom
#mkdir /opt/pydicom
#cd /opt/pydicom
#git clone https://www.github.com/pydicom/pydicom.git
#cd pydicom
#git checkout ebf6a79602348d003a1d1324c66626f9f2b05432
#python setup.py install

#dicomunwrap, will install pydicom
cd /apps
git clone https://gitlab.com/cfmm/DicomRaw
cd DicomRaw
sudo pip install -r requirements.txt

#needed when install dcm4che
apt-get install -y default-jre

#install dcm4che
cd /src
bash install_dcm4che_ubuntu.sh /opt

#For retrieving physio dicom files. without this line, all the physio series will not be retrieved with getscu
echo '1.3.12.2.1107.5.9.1:ImplicitVRLittleEndian;ExplicitVRLittleEndian' >>/opt/dcm4che-3.3.8/etc/getscu/store-tcs.properties

#########
%environment


#anaconda2
export PATH=/opt/anaconda2/bin/:$PATH

#dcm4che
export PATH=/opt/dcm4che-3.3.8/bin:$PATH

#python scripts
export PATH=/apps/cfmm2tar:$PATH
export _JAVA_OPTIONS="-Xmx2048m"

%runscript
exec cfmm2tar "$@"

Collection

• Name: khanlab/cfmm2tar
• License: GNU General Public License v3.0

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.