Installation from Source
You can try the following two options:
Option 1: Download latest stable release
You can always download the latest tarball release from Github
For example, here is how to download version
2.3.1 and install:
VERSION=2.3.1 wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz tar xvf singularity-$VERSION.tar.gz cd singularity-$VERSION ./configure --prefix=/usr/local make sudo make install
Option 2: Download the latest development code
To download the most recent development code, you should use Git and do the following:
git clone https://github.com/singularityware/singularity.git cd singularity ./autogen.sh ./configure --prefix=/usr/local make sudo make install
note: The ‘make install’ is required to be run as root to get a properly installed Singularity implementation. If you do not run it as root, you will only be able to launch Singularity as root due to permission limitations.
To update your Singularity version, you might want to first delete the executables for the old version:
sudo rm -rf /usr/local/libexec/singularity
And then install using one of the methods above.
Singularity is available on Debian (and Ubuntu) systems starting with Debian stretch and the Ubuntu 16.10 yakkety releases. The package is called
singularity-container. For recent releases of singularity and backports for older Debian and Ubuntu releases, we recommend that you use the NeuroDebian repository.
Testing first with Docker
If you want a quick preview of the NeuroDebian mirror, you can do this most easily with the NeuroDebian Docker image (and if you don’t, skip to the next section). Obviously you should have Docker installed before you do this.
First we run the
neurodebian Docker image:
$ docker run -it --rm neurodebian
Then we update the cache (very quietly), and look at the
singularity-container policy provided:
$ apt-get update -qqq $ apt-cache policy singularity-container singularity-container: Installed: (none) Candidate: 2.3-1~nd80+1 Version table: 2.3-1~nd80+1 0 500 http://neuro.debian.net/debian/ jessie/main amd64 Packages
You can continue working in Docker, or go back to your host and install Singularity.
Adding the Mirror and Installing
You should first enable the NeuroDebian repository following instructions on the NeuroDebian site. This means using the dropdown menus to find the correct mirror for your operating system and location. For example, after selecting Ubuntu 16.04 and selecting a mirror in CA, I am instructed to add these lists:
sudo wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
and then update
sudo apt-get update
then singularity can be installed as follows:
sudo apt-get install -y singularity-container
During the above, if you have a previously installed configuration, you might be asked if you want to define a custom configuration/init, or just use the default provided by the package, eg:
Configuration file '/etc/singularity/init' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. What would you like to do about it ? Your options are: Y or I : install the package maintainer's version N or O : keep your currently-installed version D : show the differences between the versions Z : start a shell to examine the situation The default action is to keep your current version. *** init (Y/I/N/O/D/Z) [default=N] ? Y Configuration file '/etc/singularity/singularity.conf' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. What would you like to do about it ? Your options are: Y or I : install the package maintainer's version N or O : keep your currently-installed version D : show the differences between the versions Z : start a shell to examine the situation The default action is to keep your current version. *** singularity.conf (Y/I/N/O/D/Z) [default=N] ? Y
And for a user, it’s probably well suited to use the defaults. For a cluster admin, we recommend that you read the admin docs to get a better understanding of the configuration file options available to you. Remember that you can always tweak the files at
/etc/singularity/init if you want to make changes.
After this install, you should confirm that
2.3-dist is the version installed:
$ singularity --version 2.3-dist
Note that if you don’t add the NeuroDebian lists, the version provided will be old (e.g., 2.2.1). If you need a backport build of the recent release of Singularity on those or older releases of Debian and Ubuntu, you can see all the various builds and other information here.
Build an RPM from source
Like the above, you can build an RPM of Singularity so it can be more easily managed, upgraded and removed. From the base Singularity source directory do the following:
./autogen.sh ./configure make dist rpmbuild -ta singularity-*.tar.gz sudo yum install ~/rpmbuild/RPMS/*/singularity-[0-9]*.rpm
Note: if you want to have the RPM install the files to an alternative location, you should define the environment variable ‘PREFIX’ to suit your needs, and use the following command to build:
PREFIX=/opt/singularity rpmbuild -ta --define="_prefix $PREFIX" --define "_sysconfdir $PREFIX/etc" --define "_defaultdocdir $PREFIX/share" singularity-*.tar.gz
autogen.sh If you get an error that you have packages missing, for example on Ubuntu 16.04:
./autogen.sh +libtoolize -c ./autogen.sh: 13: ./autogen.sh: libtoolize: not found +aclocal ./autogen.sh: 14: ./autogen.sh: aclocal: not found +autoheader ./autogen.sh: 15: ./autogen.sh: autoheader: not found +autoconf ./autogen.sh: 16: ./autogen.sh: autoconf: not found +automake -ca -Wno-portability ./autogen.sh: 17: ./autogen.sh: automake: not found
then you need to install dependencies:
sudo apt-get install -y build-essential libtool autotools-dev automake autoconf
Build a DEB from source
To build a deb package for Debian/Ubuntu/LinuxMint invoke the following commands:
$ fakeroot dpkg-buildpackage -b -us -uc # sudo will ask for a password to run the tests $ sudo dpkg -i ../singularity-container_2.3_amd64.deb
Note that the tests will fail if singularity is not already installed on your system. This is the case when you run this procedure for the first time. In that case run the following sequence:
$ echo "echo SKIPPING TESTS THEYRE BROKEN" > ./test.sh $ fakeroot dpkg-buildpackage -nc -b -us -uc # this will continue the previous build without an initial 'make clean'
Install on your Cluster Resource
In the case that you want Singularity installed on a shared resource, you will need to talk to the administrator of the resource. Toward this goal, we’ve prepared a helpful guide that you can send to him or her. If you have unanswered questions, please reach out.