49 lines
2.5 KiB
Plaintext
49 lines
2.5 KiB
Plaintext
#%Module1.0
|
|
|
|
module-whatis "3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)"
|
|
module-url "https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
|
|
module-license "GPLv2 license"
|
|
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch>"
|
|
|
|
module-help "
|
|
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
|
|
stand-alone computer program that employs an empirical Bayesian approach to
|
|
refinement of (multiple) 3D reconstructions or 2D class averages in electron
|
|
cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the
|
|
MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of
|
|
3D-reconstruction is regularised by incorporating prior knowledge: the fact
|
|
that macromolecular structures are smooth, i.e. they have limited power in the
|
|
Fourier domain. In the corresponding Bayesian framework, many parameters of a
|
|
statistical model are learned from the data, which leads to objective and
|
|
high-quality results without the need for user expertise. The underlying theory
|
|
is given in Scheres (2012) JMB. A more detailed description of its
|
|
implementation is given in Scheres (2012) JSB. If RELION is useful in your
|
|
work, please cite at least one of these papers.
|
|
|
|
Scheres(2012) JMB http://www.sciencedirect.com/science/article/pii/S0022283611012290
|
|
Scheres(2012) JSB http://www.sciencedirect.com/science/article/pii/S1047847712002481
|
|
"
|
|
|
|
setenv RELION_QUEUE_USE yes
|
|
setenv RELION_QUEUE_NAME gpu
|
|
setenv RELION_QSUB_COMMAND sbatch
|
|
setenv RELION_THREAD_MAX 44
|
|
setenv RELION_QSUB_EXTRA_COUNT 2
|
|
setenv RELION_QSUB_EXTRA1 "Max Time"
|
|
setenv RELION_QSUB_EXTRA1_DEFAULT "1-00:00:00"
|
|
setenv RELION_QSUB_EXTRA1_HELP "Maximum time before the job is killed by slurm. Default: 1-00:00:00"
|
|
setenv RELION_QSUB_EXTRA2 "Extra Slurm Args"
|
|
setenv RELION_QSUB_EXTRA2_DEFAULT ""
|
|
setenv RELION_QSUB_EXTRA2_HELP "Any additional arguments to pass to slurm"
|
|
setenv RELION_SCRATCH_DIR /scratch
|
|
setenv RELION_UNBLUR_EXECUTABLE /opt/psi/EM/Unblur/1.0.2/bin/unblur_openmp_7_17_15.exe
|
|
setenv RELION_SUMMOVIE_EXECUTABLE /opt/psi/EM/Summovie/1.0.2/bin/sum_movie_openmp_7_17_15.exe
|
|
setenv RELION_CTFFIND_EXECUTABLE /opt/psi/EM/ctffind4/4.1.8/bin/ctffind
|
|
setenv RELION_GCTF_EXECUTABLE /opt/psi/EM/Gctf/1.06/bin/Gctf
|
|
setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap
|
|
|
|
# Version-specific variables
|
|
setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/3.1-beta/scripts/multi_gpu.sh
|
|
setenv RELION_MOTIONCOR2_EXECUTABLE /opt/psi/EM/MotionCor2/1.3.0/bin/MotionCor2_1.3.0-Cuda92
|
|
|