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System Requirements
robertprior-fixstars edited this page Sep 20, 2019
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To run ExSequence the following OS and software is required:
- Linux: A Linux OS is required; testing has been done on CentOS 7.
- Bash: The main pipeline script which launches the other MATLAB scripts uses bash.
- MATLAB: Most of the functionality of ExSequence is contained in MATLAB scripts and is required
- (optional) CUDA: Allows for using NVIDIA GPUs to accelerate some stages of ExSequence pipeline.
- (optional) Python: Is used to allow for setting parameters in a GUI or an interactive command line interface. It is also necessary for using a performance profile option. Python major versions 2 and 3 are supported.
- (optional) Jupyter, numpy, pandas, matplotlib: These are additional Pyhton tools and libraries necessary for displaying the results of the performance profile.
RAM requirements depend on the size of the input dataset as well as the degree of parallelization used. Using multiple process reduces the time taken by the pipeline requires having sufficient memory.
Disk usage also depends on the input data size. The colour correction and registration stages create full copies of the data and normalization stage creates one file per round. These stages also optionally create down sampled versions further increasing the size. The input data size increases to roughly 3-4 times the original size after running the pipeline.
- 1 Setup Cluster
- 2 Color Correction
- 3 Normalization
- 4 Registration
- 5 Puncta Extraction
- 6 Base Calling
- Performance Profile
- Example Batching
- Summary Reporting (link to page) / Analysis (link to page) All of above would be bullet points but thought each folder with useful scripts in the repository would have its own page with example usages and descriptions for the files under the given directory. Unsure on this as haven't used anything under these directories directly myself (i.e not through runPipeline) apart from tests/perf-profile/summarize-stat-logs.sh. Should any of these have a separate page? Note have not made pages for this yet as not sure how many should be made or if this break down makes sense.
- Troubleshooting