pipeline:meridien:sp_polishing
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pipeline:meridien:sp_polishing [2021/03/16 10:07] aali [Reference] |
pipeline:meridien:sp_polishing [2021/03/16 10:30] aali |
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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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| ===== Output ===== | ===== Output ===== | ||
| - | + | ; shiny.star : Output star file for polishing particles. | |
| - | ; ; bdb: | + | ; bdb: |
| + | ; BDB2STAR : Using sphire2relion tool , the bdb stack is converted to star file so that it can be used in relion. The star file is saved in BDB2STAR folder. | ||
| + | ; PostProcess : Since the input to the tool is Post refiner directory, the tool can automatically create the necessary file in PostProcess folder which is necessary to provide for polishing. | ||
| ===== ===== | ===== ===== | ||
pipeline/meridien/sp_polishing.txt · Last modified: 2021/03/16 10:44 by aali
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