assman_g
18454b7782
Set MotionCor2 path based on the loaded cuda version. Closes #275 See merge request Pmodules/buildblocks!432
68 lines
3.4 KiB
Plaintext
68 lines
3.4 KiB
Plaintext
#%Module1.0
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module-whatis "3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)"
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module-url "https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
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module-license "GPLv2 license"
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module-maintainer "Greta Assmann <greta.assmann@psi.ch>"
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module-help "
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RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
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stand-alone computer program that employs an empirical Bayesian approach to
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refinement of (multiple) 3D reconstructions or 2D class averages in electron
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cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the
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MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of
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3D-reconstruction is regularised by incorporating prior knowledge: the fact
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that macromolecular structures are smooth, i.e. they have limited power in the
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Fourier domain. In the corresponding Bayesian framework, many parameters of a
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statistical model are learned from the data, which leads to objective and
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high-quality results without the need for user expertise. The underlying theory
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is given in Scheres (2012) JMB. A more detailed description of its
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implementation is given in Scheres (2012) JSB. If RELION is useful in your
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work, please cite at least one of these papers.
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Scheres(2012) JMB http://www.sciencedirect.com/science/article/pii/S0022283611012290
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Scheres(2012) JSB http://www.sciencedirect.com/science/article/pii/S1047847712002481
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"
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setenv RELION_QUEUE_USE yes
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setenv RELION_QUEUE_NAME gpu
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setenv RELION_QSUB_COMMAND sbatch
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setenv RELION_THREAD_MAX 44
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setenv RELION_QSUB_EXTRA_COUNT 2
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setenv RELION_QSUB_EXTRA1 "Max Time"
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setenv RELION_QSUB_EXTRA1_DEFAULT "1-00:00:00"
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setenv RELION_QSUB_EXTRA1_HELP "Maximum time before the job is killed by slurm. Default: 1-00:00:00"
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setenv RELION_QSUB_EXTRA2 "Extra Slurm Args"
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setenv RELION_QSUB_EXTRA2_DEFAULT ""
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setenv RELION_QSUB_EXTRA2_HELP "Any additional arguments to pass to slurm"
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setenv RELION_SCRATCH_DIR /scratch
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setenv RELION_UNBLUR_EXECUTABLE /opt/psi/EM/Unblur/1.0.2/bin/unblur_openmp_7_17_15.exe
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setenv RELION_SUMMOVIE_EXECUTABLE /opt/psi/EM/Summovie/1.0.2/bin/sum_movie_openmp_7_17_15.exe
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setenv RELION_CTFFIND_EXECUTABLE /opt/psi/EM/ctffind4/4.1.8/bin/ctffind
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setenv RELION_GCTF_EXECUTABLE /opt/psi/EM/Gctf/1.06/bin/Gctf
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setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap
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setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/topaz
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setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/python
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setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/5.0-sp/torch
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# Version-specific variables
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setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/$V/scripts/multi_gpu.sh
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# See MC2 compatibility matrix: https://intranet.psi.ch/en/bio/motioncor2
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if {[string match "8.0*" $env(CUDA_VERSION)]} {
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setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.3.2/bin/MotionCor2_1.3.2-Cuda80"
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} elseif {[string match "11.0*" $env(CUDA_VERSION)]} {
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setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2"
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} else {
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setenv RELION_MOTIONCOR2_EXECUTABLE "/opt/psi/EM/MotionCor2/1.6.4/bin/MotionCor2"
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}
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# relion 5 features
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if {[file exists /opt/psi/EM/relion/$V/conda_env/$V]} {
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setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/topaz
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setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/$V/conda_env/$V/bin/python
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}
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if {[file exists /opt/psi/EM/relion/$V/torch]} {
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setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/$V/torch
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}
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