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Installing EM Packages

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rmarabini edited this page Jul 31, 2017 · 12 revisions
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Packages installation

To install automatically the packages used by scipion, run scipion install PACKAGENAME, where PACKAGENAME can be any of the items that scipion install --help lists as "Available packages" (see below). By default, the latest available version of a package will be installed. To specify a different version simply use scipion install PACKAGENAME-VERSION

./scipion install --help
Usage: /home/gsharov/soft/scipion/scipion install [<target>] [--no-scipy] [--no-opencv] [--show]

Installs Scipion. Also used to install only part of it, as specified
in the <target>, or to add extra em packages to Scipion.

Arguments:
  <target>      a library, a python module, an em package or a xmipp file.
                Version can be specified after a hyphen (-)
   -j N         where N is the number of processors to use during installation
  --help        show this help message
  --show        just show what would be done, without actually installing
  --no-opencv   do not install opencv (big) or anything that depends on it
  --no-scipy    do not install scipy or anything that depends on it
  --no-xmipp    use this option only after a successful compilation of Xmipp
                to save some time when installing other packages

Example: scipion install eman-2.12


Available packages: ([ ] not installed, [X] seems already installed)
     Gautomatch      0.53 [ ]
           Gctf      0.50 [ ]     1.06 [ ]
...
         simple       2.1 [X]
         spider     21.13 [X]    24.02 [X]
       summovie     1.0.2 [X]
         unblur    1.0.15 [ ]    1.0.2 [X]

Below you can find additional information on each package specifics. For example, how to solve a compilation issue.

Xmipp

Supported versions: 3.2 (Jan-2016)

Xmipp is now integrated in Scipion. There is no need to install it separately. The biggest difference with version 3.1 is that all protocols have been ported to Scipion together with the installation of external libraries.

SPIDER

Supported versions: 21.13 (Dec 2013)

Details:

  • spider depends on csh at runtime

  • Check that a link was properly created in software/em/spider anchor-link

Relion

Supported versions: 1.3 (Aug 2014), 1.4, 1.4-float (Sep 2015)

Details:

  • relion depends on FLTK library. The version included depends on libpng15. If FLTK compilation fails due to missing "png_set_longjmp_fn", then:

    • install libpng15 to /usr/local 2. Update your CFLAGS and LDFLAGS: <verbatim> export CFLAGS=-I/usr/local/include export LDFLAGS=-L/usr/local/lib </verbatim> 3. Recompile relion again (scipion install relion-1.4 or similar)

EMAN

Supported versions: 2.11 (Jun 2015), 2.12 (Oct 2015)

Details:

  • Check that a link was properly created in software/em/eman2.11 and/or software/em/eman2.12

CCP4

Since CCP4 installation requires to sign a licence agreement we have not included this package in the installation script. Please install it as described in http://www.ccp4.ac.uk/download/#os=linux and then follow the instruction of the link[link] (Linking to existing package installations) section anchor-link

Linking to existing package installations

If you want to use existing installations of your packages instead of having Scipion install them for you, just go to the software/em directory and create a symbolic link with the exact name of the package as Scipion expects it.

For example:

.../scipion/software/em$ ls -l
total 0
lrwxrwxrwx 1 scipion scipion 48 Mar 25 15:58 bsoft -> /home/scipion/buildbot/scipion_packages/em/bsoft
lrwxrwxrwx 1 scipion scipion 50 Mar 25 15:58 ctffind -> /home/scipion/buildbot/scipion_packages/em/ctffind
lrwxrwxrwx 1 scipion scipion 47 Mar 25 15:58 eman -> /home/scipion/buildbot/scipion_packages/em/eman
lrwxrwxrwx 1 scipion scipion 51 Mar 25 15:58 frealign -> /home/scipion/buildbot/scipion_packages/em/frealign
lrwxrwxrwx 1 scipion scipion 49 Mar 25 15:58 relion -> /home/scipion/buildbot/scipion_packages/em/relion
lrwxrwxrwx 1 scipion scipion 49 Mar 25 15:58 spider -> /home/scipion/buildbot/scipion_packages/em/spider
lrwxrwxrwx 1 scipion scipion 48 Mar 25 15:58 xmipp -> /home/scipion/buildbot/scipion_packages/em/xmipp
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