Installing EM Packages

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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":

./scipion install --help
usage: ./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
  --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

Available packages (*: seems already installed)
  bsoft
  chimera
  cryoem
...
  spider
  motioncorr
  simple

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

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