adding parsnp 2.0.5 - Githubissues

erinyoung commented 3 months ago

There's a new version of parsnp!

Parsnp now outputs a MAF file in addition to the typical XMFA file (can turn this off with (--no-maf). Parsnp now uses the partition mode by default when there are more than 100 input sequences.

All I did was copy the Dockerfile from version 2.0.4 and update the software arg.

The full diff:

$ diff parsnp/2*/Dockerfile
1c1
< ARG PARSNP_VER="2.0.4"
---
> ARG PARSNP_VER="2.0.5"

Pull Request (PR) checklist:

[X] Include a description of what is in this pull request in this message.
[X] 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 )
[X] 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)
- [X] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
[X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
- [X] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
[X] Dockerfile includes the recommended LABELS
[X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
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Kincekara commented 3 months ago

@erinyoung I realized that parsnp searches FastTreeMP which can improve overall performance. Have you tried to install FastTreeMP instead of Fasttree?

#26 72.27 19:59:06 - INFO - FastTreeMP not found. Trying fasttree...
#26 72.27 19:59:06 - DEBUG - fasttree -nt -quote -gamma -slow -boot 100 outdir_parsnp_fasttree/parsnp.snps.mblocks

erinyoung commented 3 months ago

I'm going to pass installing FastTreeMp (http://www.microbesonline.org/fasttree/#OpenMP) because it involves installing fasttree from source instead of just downloading the executable.

Kincekara commented 3 months ago

@erinyoung precompiled executable is available here: http://www.microbesonline.org/fasttree/FastTreeMP I am merging this now. We can check FastTreeMP in the next iteration.

Kincekara commented 3 months ago

Thank you for the update! Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9191921039.

StaPH-B / docker-builds

adding parsnp 2.0.5 #980