https://github.com/cytomining/cytominer-vm
[DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster
Science Score: 10.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
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Repository
[DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster
Basic Info
Statistics
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 4
- Releases: 0
Topics
Metadata Files
README.md
This package is deprecated and will no longer be supported. Please use at your own risk!
VM for profiling
This packer configuration creates a VM provisioned with tools need for profiling analysis.
- Python packages
- cytominer-database and dependencies
- Distributed-CellProfiler and dependencies
In addition, it mounts - an S3 bucket so that CellProfiler can access files - an NFS (Amazon Elastic File System (EFS))
Install packer
OS X:
brew install packer
Windows: - Get it here
Building the VM
Authenticate
aws configure
Edit EFS and S3 configurations
Edit EFS_ID in efs.sh, and S3_ROLE and BUCKET_ID is s3.sh
appropriately.
Validate and build
Note that although instance specifics are included in cytominer_ami.json
(c4.large), and an instance will be created, the instance only exists to
create the AMI and will be destroyed upon completion,
delete_on_termination: true, leaving only the newly created AMI.
packer validate cytominer_ami.json
Specify security_group_ids, subnet_id and vpc_id on which the builder
should be run (get these from AWS console)
packer build -var 'security_group_ids=sg-NNNNNNNN,sg-NNNNNNNN' -var 'subnet_id=subnet-NNNNNNNN' -var 'vpc_id=vpc-NNNNNNNN' cytominer_ami.json
The security groups should be such that together they allow - SSH access on port 22 - NFS access on part 2049 (for EFS)
Owner
- Name: cytomining
- Login: cytomining
- Kind: organization
- Repositories: 27
- Profile: https://github.com/cytomining
GitHub Events
Total
Last Year
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Shantanu Singh | s****h@b****g | 33 |
| Gregory Way | g****y@g****m | 1 |
| Beth Cimini | b****7 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 6
- Total pull requests: 3
- Average time to close issues: over 1 year
- Average time to close pull requests: 5 months
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 2.17
- Average comments per pull request: 0.67
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- shntnu (3)
- bethac07 (2)
- mtegtmey (1)
Pull Request Authors
- shntnu (2)
- bethac07 (1)