Add bindashtree v0.1.0 #1146
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Add bindashtree v0.1.0 #1146
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…ds into tkp-bindashtree
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It looks like the tests worked |
erinyoung
reviewed
Dec 26, 2024
bindashtree/0.1.0/README.md
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| ``` | ||
| Binwise Densified MinHash and Rapid Neighbor-joining Tree Construction | ||
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| Usage: bindashtree [OPTIONS] --input <INPUT_LIST_FILE> --output_tree <OUTPUT_TREE_FILE> | ||
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| Options: | ||
| -i, --input <INPUT_LIST_FILE> | ||
| Genome list file (one FASTA/FNA file per line), gz supported | ||
| -k, --kmer_size <KMER_SIZE> | ||
| K-mer size [default: 16] | ||
| -s, --sketch_size <SKETCH_SIZE> | ||
| MinHash sketch size [default: 10240] | ||
| -d, --densification <DENS_OPT> | ||
| Densification strategy: 0=Optimal Densification, 1=Reverse Optimal Densification/faster Densification [default: 0] | ||
| -t, --threads <THREADS> | ||
| Number of threads to use in parallel [default: 1] | ||
| --tree <TREE_METHOD> | ||
| Tree construction method: naive, rapidnj, hybrid [default: rapidnj] | ||
| --chunk_size <chunk_size> | ||
| Chunk size for RapidNJ/Hybrid methods [default: 30] | ||
| --naive_percentage <naive_percentage> | ||
| Percentage of steps naive for hybrid method [default: 90] | ||
| --output_matrix <OUTPUT_MATRIX_FILE> | ||
| Output the phylip distance matrix to a file | ||
| --output_tree <OUTPUT_TREE_FILE> | ||
| Output the resulting tree in Newick format to a file | ||
| -h, --help | ||
| Print help | ||
| -V, --version | ||
| Print version | ||
| ``` |
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This looks like the printed help message. I'm not going to make you change this, but I recommend following the format of
# <program> container
Main tool: [<program>](link to program)
Code repository: <url for code>
Additional tools:
- list: version
Basic information on how to use this tool:
- executable: <tool>
- help: <-h>
- version: <-v>
- description: <tool does something>
Additional information:
<Container contains X database at Y>
Full documentation: link to documentation or wiki
Because it helps some of the external parsers.
erinyoung
reviewed
Dec 26, 2024
bindashtree/0.1.0/Dockerfile
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| # Copy built binaries from the builder stage | ||
| COPY --from=builder /bindashtree-${BINDASHTREE_VER}/target/release/bindashtree /usr/local/bin/ | ||
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Could you add a CMD line and WORDIR line at the end of the 'app' stage?
It'd be something like
CMD ["bindashtree", "--help"]
WORKDIR /data
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ok added it in the latest commit, thanks for the help!
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This looks great! But it does look like the 'app' stage is missing the CMD and WORKDIR layers. Can you add them? |
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@taylorpaisie , I don't want to cause you any kind of alarm, but we updated the file structure of the repo... which probably messed you up in all kinds of ways WE ARE SO SORRY But also... there wasn't a great time to do it. Thank you for your efforts. Dockerfiles and READMEs are now in Also, this may mean that there are more GA errors. PLEASE LET US KNOW IF YOU ENCOUNTER THEM!!! |
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The tests still work |
erinyoung
approved these changes
Dec 30, 2024
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Thank you for putting this together! You can check the status of the deployment at https://github.com/StaPH-B/docker-builds/actions/runs/12550397445 |
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Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)