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pipeline:meridien:sp_polishing [2021/03/16 10:01] aali [Output] |
pipeline:meridien:sp_polishing [2021/03/16 10:15] aali [Typical usage] |
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: After running the polishing routine, the wrapper automatically converts the shiny.star in | : After running the polishing routine, the wrapper automatically converts the shiny.star in | ||
the Output folder to a BDB stack and saves it in the folder name of Polish Stack. | the Output folder to a BDB stack and saves it in the folder name of Polish Stack. | ||
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- | : | ||
</ | </ | ||
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; %%--%%training_params : In case if the user wants to do the training part of the polishing then this is None. Otherwise provide the optimize_params.txt file. (default none) | ; %%--%%training_params : In case if the user wants to do the training part of the polishing then this is None. Otherwise provide the optimize_params.txt file. (default none) | ||
; %%--%%min_no_particles : Number of particles to inlcude for training. (default 5000) | ; %%--%%min_no_particles : Number of particles to inlcude for training. (default 5000) | ||
- | ; %%--%%submission_template : Submission template for mpi command (default none) | + | ; %%--%%submission_template : Submission template for MPI command. In case of running this tool on a cluster, always a submission template. The number of MPI processors and threads in the submission template should be the same as the one specified below in the MPI procs and threads value.(default none) |
; %%--%%submission_command : Submission commmand for cluster (default sbatch) | ; %%--%%submission_command : Submission commmand for cluster (default sbatch) | ||
; %%--%%relion_mpirun_executable : Since there can be more than one mpirun environment installed on a workstation or on a cluster. It can be sometimes necessary to provide the relion specific mpirun executable. Just type which mpirun -a in a terminal and choose the one which relion requires. (default mpirun) | ; %%--%%relion_mpirun_executable : Since there can be more than one mpirun environment installed on a workstation or on a cluster. It can be sometimes necessary to provide the relion specific mpirun executable. Just type which mpirun -a in a terminal and choose the one which relion requires. (default mpirun) | ||
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==== Reference ==== | ==== Reference ==== | ||
- | Zivanov | + | Jasenko |
==== Developer Notes ==== | ==== Developer Notes ==== | ||