Page Index - ccdmb/predector GitHub Wiki

68 page(s) in this GitHub Wiki:

• Home
• Predector
• Table of contents
• Quick install
• Requirements
• Optional - Remove previous software environments for old versions of the pipeline
• 1. Install Conda, Docker, or Singularity
• 2. Download the proprietary software dependencies
• 3. Build the conda environment or container
• 4. Install NextFlow
• 5. Test the pipeline
• Extended dependency install guide
• Building the conda environment the long way
• Building the Docker container the long way
• Building the Singularity container the long way
• Copying environments to places where you don't have root user permission
• Running the pipeline
• Command line parameters
• Manual ranking scores
• Profiles and configuration
• Profiles
• Custom configuration
• Running different pipeline versions.
• Providing pre-downloaded Pfam, PHI-base, and dbCAN datasets.
• Providing pre-computed results to skip already processed proteins
• Accessing and copying results
• Cleaning up
• Pipeline output
• deduplicated/
• analysis_software_versions.tsv
• *-ranked.tsv
• *.gff3
• Individual results tables
• *.ldjson
• pipeline_info/
• Linking vs copying results.
• Mapping results to genomes coordinates for genome browsers
• Common issues
• Cannot find revision X.X.X -- Make sure that it exists in the remote repository https://github.com/ccdmb/predector
• Running with docker Unable to find image 'predector/predector:X.X.X' locally
• Running with singularity ERROR : Failed to set loop flags on loop device: Resource temporarily unavailable.
• Connecting to XXX... failed: Connection timed out.
• ERROR ~ unable to resolve class XXX
• Running/setting up conda environment: loadable library and perl binaries are mismatched (got handshake key 0xdb80080, needed 0xde00080)
• Error while running signalp 6 ValueError: zero-size array to reduction operation maximum which has no identity
• Error while running a process with Command exit status: 137
• Installing with Mamba, Problem: nothing provides __glibc >=2.17,<3.0.a0 needed by...
• FAQ
• What do Predector "effector scores" actually mean?
• How should I cite Predector?
• 1.0.0
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• 1.1.1
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• 1.2.1
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• 1.2.2
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• 1.2.3
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• 1.2.4
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• 1.2.5
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• 1.2.6
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• 1.2.7
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