Dear All,
How can I get the commands that get executed for the processing. Say - Unblur is used for aligning the movies- what is the command used for that.
Thanks
Andy
Dear All,
How can I get the commands that get executed for the processing. Say - Unblur is used for aligning the movies- what is the command used for that.
Thanks
Andy
Hi Andy,
Most programs are named as literally as possible. In your example, it is "unblur" (all lowercase) which will then give you a series of command line prompts for the options. This is of course assuming cistem is on your path. If you are using the precompiled binary, you can find the programs in the same directory as "cistem". You should have:
align_symmetry calculate_fsc ctffind mag_distortion_correct montage refine3d resize unblur
applyctf cisTEM display make_orth_views prepare_stack remove_inf_and_nan scale_with_mask
apply_gain_ref cisTEM_job_control estimate_dataset_ssnr make_size_map project3d remove_outlier_pixels sharpen_map
apply_mask console_test extract_particles merge2d reconstruct3d resample sum_all_mrc_files
calc_occ convert_tif_to_mrc find_particles merge3d refine2d reset_mrc_header sum_all_tif_files
Each command line option has a default and a short message explaining what it does (at the prompt.)
These can be easily scripted.
HTH
Ben
Hi Ben,
Thanks. I do see all the programs in the cisTEM folder and on the terminal when the programs are invoked the options (input etc) do appear. What I am trying to get is there a way to see all the options and the usage of the program say
type the program and hit return -- it provides the usage and the options
or anything similar, say
program -help
Andy
Hi Andy,
Unfortunately no, there is not (save for ctffind and simulate).
The reason for this relates to the way the cisTEM gui dispatches jobs over sockets, which in turn means most of our programs do not take command line options, with the noted exceptions above. Perhaps a step in the right direction would be to at least put the sort of information you are looking for on either the cisTEM webpage (cistem.org) or on the cisTEM_docs page.
I don't have time to sit and define all of these at once, but would be happy to write up one or two and send you a link if you have specific programs you are interested in?
Cheers
Ben
Hi Andy,
I have documented most of the programs available in cisTEM 1.0 beta, you can find the info here.
I also discuss it and suggested use cases on this you tube vid.