pndni/development-image:dev
$ singularity pull shub://pndni/development-image:dev
Singularity Recipe
Bootstrap: shub
From: pndni/minc-ants-fsl-and-fs-container:1.1.0
# OSVersion: 7
# MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/x86_64/
# Include: yum
#
%post
mkdir -p /scratch
mkdir -p /project
##############################
# python stuff #
# ############################
yum install -y epel-release
yum install -y python36 python36-pip python36-devel libstdc++-static pigz python36-virtualenv python36-scipy python36-numpy python36-pytest python36-pytest-cov python36-psutil python36-sphinx
virtualenv-3.6 /opt/pythonenv
source /opt/pythonenv/bin/activate
pip install heudiconv
pip install nipype[all]
pip install nibabel
deactivate
%apphelp all
Set up environment for minc, ants, freesurfer, FSL,
dcm2niix, and python environment
Using freesurfer requires a freesurfer license file.
A license file may be obtained from
https://surfer.nmr.mgh.harvard.edu/registration.html
Ensure that the license file is visible from the container,
and set the environment variable FS_LICENSE to point to it
(or copy the file to /opt/freesurfer/license.txt from
inside the container)
%appenv pythonenv
source /opt/pythonenv/bin/activate
%appenv heudiconv
source ${SCIF_APPENV_dcm2niix}
source ${SCIF_APPENV_pythonenv}
%apprun heudiconv
heudiconv "$@"
%appinstall dcm2niix
git clone --branch v1.0.20190410 https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
/opt/cmake/bin/cmake -DCMAKE_INSTALL_PREFIX=/opt/dcm2niix ..
make
make install
rm -rf dcm2niix
%appenv dcm2niix
export PATH=/opt/dcm2niix/bin:$PATH
%apprun dcm2niix
dcm2niix "$@"
%appenv all
source $SCIF_APPENV_freesurfer_nominc
source $SCIF_APPENV_fsl
source $SCIF_APPENV_minc
export PATH=/scif/apps/ants/bin:$PATH
source $SCIF_APPENV_pythonenv
%labels
Maintainer Steven Tilley
Version dev
Collection
- Name: pndni/development-image
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/pndni-development-image-dev |
collection name | pndni/development-image |
branch | master |
tag | dev |
commit | 8fc07a399ca25d00487db7046f9f8293c0f71674 |
version (container hash) | 45d98e3c85fc4b8b12866b911c520088 |
build date | 2019-04-13T15:19:00.989Z |
size (MB) | 27099 |
size (bytes) | 10970685471 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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