Warp is a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

References:

• Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods. 2019 Nov;16(11):1146-1152.
• Warp github page:
  https://github.com/warpem/warp

• Warp User Guides:
  https://warpem.github.io/warp/user_guide/warptools/quick_start_warptools_tilt_series/

• WarpTools expects raw tilt series data as individual movies, or as individual motion-corrected images, but not as combined tilt series stacks. The mdoc files containing the metadata for each tilt series. If only tilt series stacks (instead of individual movies) are available, load warp on Biowulf and copy the following python scrip to split tilt series stacks for processing in WarpTools:https://warpem.github.io/warp/reference/warptools/processing_tilt_series_stacks/#running-the-script

Allocate an interactive session and run the program. Please check the above User Guides documentation for detailed tutorial examples.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=gpu:p100:1 --mem=16g -c8 
salloc.exe: Pending job allocation 44219178
salloc.exe: job 44219178 queued and waiting for resources
salloc.exe: job 44219178 has been allocated resources
salloc.exe: Granted job allocation 44219178
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn2364 are ready for job
[user@cn2364 ~]$ WarpTools --help
[user@cn2364 ~]$ MTools --help
[user@cn2364 ~]$ MCore --help
[user@cn2364 ~]$ EstimateWeights --help
[user@cn2364 ~]$ WarpWorker --help
[user@cn2364 ~]$ Noise2Map --help
[user@cn2364 ~]$ Noise2Mic --help
[user@cn2364 ~]$ Noise2Tomo --help

An example of warp cryo-ET template matching with a template from the EMDB: (user input in bold):

[user@biowulf]$ cat << 'EOS' > template_matching.sh
> #!/bin/bash
> ml warp
> WarpTools ts_template_match \ 
> --settings warp_tiltseries.settings \ 
> --tomo_angpix 10 \ 
> --subdivisions 3 \ 
> --template_emdb 15854 \ 
> --template_diameter 130 \ 
> --symmetry O \ 
> --whiten \ 
> --check_hand 2 
> EOS
[user@biowulf]$ sbatch --partition=gpu --gres=gpu:p100:1 -c8 --mem=16g template_matching.sh