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adding usher version 0.6.3 #1014

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adding usher version 0.6.3 #1014

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erinyoung
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@erinyoung erinyoung commented Jun 28, 2024 •
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I find usher really useful in adding tips onto already large trees.

Usher is part of pangolin and is available on biocontainers.

This image attempts a builder stage to reduce the size. Right now, it's not building correctly - which is why this is a draft PR.

Anyone is welcome to finish this PR off.

Closes #749

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@erinyoung erinyoung mentioned this pull request Oct 28, 2024
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I have adjusted the Dockerfile and usher now installs from conda instead of attempting to be built from source.

Everything seems to run fine now

#13 [test  5/10] RUN usher -t test/global_phylo.nh -v test/global_samples.vcf -o global_assignments.pb -d output/
#13 0.061 Initializing 4 worker threads.
#13 0.061 
#13 0.062 Loading input tree.
#13 0.062 Completed in 1 msec 
#13 0.062 
#13 0.063 Loading VCF file.
#13 0.063 Completed in 0 msec 
#13 0.063 
#13 0.063 Computing parsimonious assignments for input variants.
#13 0.063 At variant site 186
#13 0.063 At variant site 187
#13 0.063 At variant site 198
#13 0.064 At variant site 203
#13 0.064 At variant site 207
#13 0.064 At variant site 210
#13 0.064 At variant site 241
#13 0.064 At variant site 285
#13 0.065 At variant site 313
#13 0.065 At variant site 398
#13 0.065 At variant site 514
#13 0.065 At variant site 490
#13 0.065 At variant site 583
#13 0.065 At variant site 614
#16 0.064 
#16 0.064 Creating output directory.
#16 0.064 
#16 0.064 Found 5 missing samples.
#16 0.064 
#16 0.064 Adding missing samples to the tree.
#16 0.066 Current tree size (#nodes): 354	Sample name: Sample1	Parsimony score: 1	Number of parsimony-optimal placements: 1
#16 0.066 Completed in 0 msec 
#16 0.066 
#16 0.066 Current tree size (#nodes): 355	Sample name: Sample2	Parsimony score: 1	Number of parsimony-optimal placements: 1
#16 0.066 Completed in 1 msec 
#16 0.066 
#16 0.066 Current tree size (#nodes): 357	Sample name: Sample3	Parsimony score: 0	Number of parsimony-optimal placements: 1
#16 0.066 Completed in 0 msec 
#16 0.066 
#16 0.066 Current tree size (#nodes): 359	Sample name: Sample4	Parsimony score: 1	Number of parsimony-optimal placements: 1
#16 0.066 Completed in 0 msec 
#16 0.066 
#16 0.067 Current tree size (#nodes): 360	Sample name: Sample5	Parsimony score: 0	Number of parsimony-optimal placements: 1
#16 0.067 Completed in 0 msec 
#16 0.067 
#16 0.067 Writing uncondensed final tree to file /test/usher-0.6.3/output4//uncondensed-final-tree.nh 
#16 0.067 The parsimony score for this tree is: 503 
#16 0.067 Completed in 1 msec 
#16 0.067 
#16 0.067 Writing mutation paths to file /test/usher-0.6.3/output4//mutation-paths.txt 
#16 0.067 Completed in 0 msec 
#16 0.067 
#16 DONE 0.1s

@erinyoung erinyoung marked this pull request as ready for review February 13, 2025 21:12
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[Container Request]: USHER
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@erinyoung