Installation Script

tranquilinho edited this page Feb 23, 2016 · 10 revisions
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This page will explain the Scipion installation system


This section contains advance installation topics that can be useful for developers.

Repository at GitHub

For developers, use this git clone command instead:

git clone

The Scipion repository was moved from SourceForge to GitHub (May-2015). If you had a git clone with the previous Sourceforge address, please update the repository with the following command:

git remote set-url origin

Installing python modules

The modules required in a typical production installation are handled in install/

Some of these modules utility is restricted to specific cases, so you may need to install them "by hand" after the standard scipion installation. For example,

scipion install pip

If you are in development mode and need a quick and dirty installation of some new python module, you can use scipion pip to install it:

scipion run pip install trendy_python_lib

When the module integration into scipion has been approved, it will be integrated in install/ as others before it.

Modifying installation script

Scipion installs several external libraries (like Python, …​) and Python modules from scratch, mainly using the scripts and The latter contains a list of external libraries, versions, and Python modules to be installed and their dependencies. To add new libraries or change to new versions, check how to change the installation script.

Generating Binaries

We generate a binary version of Scipion that can be moved as a whole and work in basically any machine without recompiling. For that purpose, we use the --binary flag when installing from a fresh download and compile in an old Linux for libc compatibility. More details here about how to generate binaries.

Installing on Mac

The following page contains our notes on the (not yet available) installation on Macs.

Install howtos for clusters

Installation Script Details


  • script. Responsible for downloading, unpacking, and installing SCons under the software/install folder. It also sends the output to a log file and stdout.

  • scipion script. Everything in Scipion is centralized through this script. This is done to ensure that the environment is controlled and to simplify the user’s experience by giving him only one file to look in for searching Scipion actions.


Let’s think of the typical installation scenarios as exercises:

  • Exercise 1: You need the Scipion path to have an additional python module in its self-compiled Python. How can you add it to Scipion python?

  • Exercise 2: To fix the version of a specific external library, you’ve decided to compile it with Scipion, so a shared library will be placed in the software/lib folder, using it whenever you use Scipion. How can you do it?

  • Exercise 3: A new EM Package, called TRFEMP (The Really Fantastic EM Package) has appeared, and you don’t want to miss the opportunity to test it with Scipion and compare the results with the other EM Packages in the market. How can you add it?


In most cases, it will be enough to take a look at the definitions of packages currently in use, in the file install/ The script is organized to reflect the 3 scenarios (library, python module, EM package)

If you need to add (or modify) low-level features, install/ is your file.

Solution to exercise 1

In Exercise 1, the solution would be very simple. Let’s say you’re trying to add the python module paramiko. With every library, every module, and every EM package in Scipion, there is always a parameter called "default" that determines whether the library, module or package has to be built by default with Scipion. That means that if the user doesn’t specify anything, the job will be done. In other case, an option called "--with-name", with 'name' being the name of the library, module, or package, will be added to the installation parameters, so the user would be able to use, for example, ./scipion install --with-paramiko. Let’s say we don’t need paramiko by default, but certain installations may need to install it, then default=false.

The addModule() function has the following parameters:

  • name: the name of the module. 'paramiko' in this case. It is mandatory.

  • tar: the compressed file to download with the sources. In case you don’t provide it, it will assume name.tgz.

  • buildDir: the name of the decompressed folder. The tarfile must contain a folder with the module, and that may not be "name", so if you don’t provide it, this will remove "tar.gz" or "tgz" from the tarfile and assume the name of the folder is that.

  • targets: SCons builders (or pseudo-builders) need targets to work. That is how it builds its dependency tree. A builder generates a list of targets which will probably be sources for the next builders in the dependency tree. An adequate target would be a file/folder that is mandatorily generated by the build process. For example, in a python module, a folder is usually generated inside lib/pythonX.Y/site-packages/ with the name of the module. That is the trick used by addModule() function. When you provide a target, it makes the untar process dependent on the download one, and the " install" will depend on the untar result, and on the other hand, will generate as a target the folder software/lib/python2.7/site-packages/name , with 'name' being the target passed as argument. If no target is passed, then 'name' will be assumed.

  • url: the URL used to download the tarfile. If no URL is provided, then will be assumed.

  • flags: the arguments that may be necessary to pass to the Python install call. In any case, --prefix=software will be assumed, so every module will be built in the Scipion architecture.

  • deps: the other elements on which this module may depend. Usually other builders' targets may be passed here. Every python module (as it may be obvious) depends on Python itself.

  • default: the yet-to-be-explained default mechanism. If nothing is passed, True is assumed (meaning the module will be built by default).

So taking everything into account, it seems like adding paramiko module, would only need to write (in SConscript file) the following line.


This means that if the user runs ./scipion install --with-paramiko, then a so-called paramiko python module is downloaded from URL to the software/tmp folder, decompressed as software/paramiko/paramiko-1.14.0 and then software/bin/python install --prefix=software will be executed, installing the module under software/lib/python2.7/site-packages/paramiko. The resulting log will be stored at software/log/paramiko.log. All those actions will be committed just by adding that simple line.

But…​ just a moment…​ wasn’t it AddModule() instead of addModule()? Yes, don’t panic. In this case, we’ve also supplied a function called addModule in the SConscript file, just to avoid needing to introduce deps=[python] (automatically adding python dependency). But please, note that it is the same as typing the line:


Solution to exercise 2

Exercise 2 is also simple and is an example of how can we compile a new external library. In this case, developer will only need to add a line in SConscript, but this time it will be a call to AddLibrary(). Let’s say it’s the sqlite library. If we see the AddLibrary() params…​

  • name: similar to AddModule; this will be 'sqlite'.

  • tar: same as in AddModule; this time we will use 'sqlite-3.6.23.tgz'. If we don’t say anything, it would look for 'sqlite.tgz'

  • buildDir: as in AddModule, it will be generated automatically as 'sqlite-3.6.23' taking it from tar name without the extension.

  • targets: in libraries, we will expect the build process to generate a shared library. Starting from software folder, the targets will be taken here. So in this case we will use 'lib/' (we know that installation procedure will generate that file).

  • url: as in AddModule, in this case URL can be also guessed, but this time the guessed address will be ('name' being 'sqlite' in our case).

  • flags: as we want to pass, during ./configure process, the line "./configure CPPFLAGS=-w CFLAGS=-DSQLITE_ENABLE_UPDATE_DELETE_LIMIT=1", we will set flags like flags=['CPPFLAGS=-w', 'CFLAGS=-DSQLITE_ENABLE_UPDATE_DELETE_LIMIT=1'].

  • autoConfigTarget: this is very specific for AutoConfig builder. As a result of the ./configure execution, some files will be generated, and those files modification will be used to detect whether or not the make order must be rebuilt. For that purpose, you can pass a specific target. Usually this target is the Makefile itself, so by default, if we don’t say anything, 'Makefile' will be used.

  • deps: same behavior as in AddModule, but in this case, no dep is asumed by default.

  • default: if nothing is passed, True is assumed.

We can then write, to solve the exercise, the following line in SConscript:

sqlite = env.AddLibrary(

That line will cause scons execution to download to software/tmp folder, then unpacked to software/tmp/sqlite-3.6.23 folder, then configured with the order "./configure 'CPPFLAGS=-w CFLAGS=-DSQLITE_ENABLE_UPDATE_DELETE_LIMIT=1'" and finally executed 'make install' on that folder. The resulting log will be stored at software/log/sqlite_configure.log and software/log/sqlite_make.log

Solution to exercise 3

The exercise 3 aims at building a new EM Package called 'TRFEMP'. In this case we will use the AddPackage() pseudo-builder. This one has the arguments described below:

  • name: As usual, we need a key to name the package. In this case, we will use 'TRFEMP'

  • tar: Same behavior as in the other pseudo-builders. If we don’t say anything, it will assume the file 'TRFEMP.tgz'.

  • buildDir: Imagine that TRFEMP packages a folder named trfemp-1.0, and inside it, there’s a Unix folder, where the configure script is placed. Then buildDir will be 'trfemp-1.0/unix'. If we don’t pass any parameters, TRFEMP would be used.

  • url: As we placed this file in address, there’s no need to explicitly indicate the URL. It will be automatically generated.

  • extraActions: Packages follow a workflow that is a little bit different from modules and libraries. They’re not supposed to compile as usual with ./configure && make && make install, but they’re supposed to be a little bit complicated. In case the compilation can be driven unattended, then there’s a way to provided the orders to Scipion installer and let it compile. Otherwise, or just because we already have the package compiled in our system, there is a way to automatically link an already present and compiled package, and this is by using the option --with-name=/path/to/package/home (using package name instead of "name" and the proper path). In that case there will be a link created in software/em/name pointing to that installation. Now imagine that TRFEMP can be simply compiled by executing 2 commands. The first one is "./configure --funny-option", and among others, that command generates a Makefile, which can be executed by using "make --very-funny-option" creating a trfemp binary. The extraActions param expects a list of tuples. Each tuple is built in the form (target, command), so in this case, we would configure extraActions=[('Makefile', './configure --funny-option'), ('trfemp', 'make --very-funny-option')].

  • deps: Deps will behave as usually.

  • default: Like the rest of the cases.

To include the TRFEMP Package, add to install/ something like…​

               extraActions=[('Makefile', './configure --funny-option'),
                                     ('trfemp', 'make --very-funny-option')],

If the TRFEMP package is not installed, executing ./scipion install TRFEMP will proceed with the download, unpacking, etc.


Xmipp is installed by default with a similar philosophy: scipion uses install/ to call install/ runs SCons using scipion environment (python binary, variables, etc).

Actual Xmipp installation steps (following SCons conventions) are defined in software/em/xmipp/scipion_sconscript

Most of the configuration of Xmipp compilation is done with environment variables. For example, if you need to specify CUDA settings, you can define the variables CUDA_SDK_PATH, CUDA_LIB_PATH and CUDA. As usual, it is easier to set those variables in the scipion config files. Again, for CUDA it would mean to edit scipion.conf, set CUDA to True (and change the other variables if needed).

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