From f17d83d3915ff1fd0e584b52fc9efc171e5154a4 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 16 Nov 2021 17:01:28 -0600 Subject: [PATCH] Replace generic README with specific one Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- README.md | 120 ++++++++++++++++++------------------------------------ 1 file changed, 39 insertions(+), 81 deletions(-) diff --git a/README.md b/README.md index ca2dea0..33bdc9a 100644 --- a/README.md +++ b/README.md @@ -1,94 +1,52 @@ -

- Logo -

+# NanoSim -# Singularity Builds +[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/nanosim) +[![NanoSim source](https://img.shields.io/static/v1?label=NanoSim%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/bcgsc/NanoSim) +[![Version 3.0.2](https://img.shields.io/static/v1?label=Latest%20version&message=1.99.2&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/nanosim) +[![Docs](https://img.shields.io/static/v1?label=Docs&message=README&color=blue&style=flat-square)](https://github.com/bcgsc/NanoSim/blob/master/README.md) +[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/) -[![Sylabs Cloud Library](https://img.shields.io/static/v1?label=Sylabs%20Cloud%20Library&message=millironx/default&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default) -[![MIT License](https://img.shields.io/github/license/MillironX/singularity-builds?style=flat-square)](https://github.com/MillironX/singularity-builds/blob/master/LICENSE.md) +NanoSim is a fast and scalable read simulator that captures the +technology-specific features of ONT data, and allows for adjustments upon +improvement of nanopore sequencing technology. -Definition files for building [Nextflow]-compatible [Singularity] container -images to use in bioinformatics pipelines. Programs get containers in this -repository if I can't find an up-to-date container that also has Nextflow's -dependencies installed (usually `bash` and `ps` are the culprits). All of these -images are available on the [Sylabs Cloud Library] for easy access. +## Tools installed -## Get started +### Minimap2 -1. [Install Singularity] -2. Enter the container, e.g. +- `minimap2` - ```bash - singularity shell library://millironx/default/julia:latest - ``` +### LAST -3. Execute commands, e.g. +- `lastdb` +- `lastal` +- `last-split` +- `last-merge-batches` +- `last-pair-probs` +- `lastdb8` +- `lastal8` +- `last-split8` +- `fastq-interleave` +- `last-dotplot` +- `last-map-probs` +- `last-postmark` +- `last-train` +- `maf-convert` +- `maf-join` +- `maf-sort` +- `maf-swap` +- `parallel-fasta` +- `parallel-fastq` - ```shellsession - Singularity> julia - _ - _ _ _(_)_ | Documentation: https://docs.julialang.org - (_) | (_) (_) | - _ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help. - | | | | | | |/ _` | | - | | |_| | | | (_| | | Version 1.6.1 (2021-04-23) - _/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release - |__/ | +### Samtools - julia> - ``` +- `samtools` -## Where else to find container images +### GenomeTools -### State Public Health Bioinformatics (StaPH-B) Dockerfiles +- `gt` -[:globe_with_meridians: Website](https://staph-b.github.io/) - -[:octocat: GitHub](https://github.com/StaPH-B/docker-builds) - -[:whale: Docker hub](https://hub.docker.com/u/staphb) +### NanoSim -All of these images are tested for Nextflow and Singularity compatability, and -are updated on a regular basis. I've even contributed to their repository. - -### Niema Moshiri's Dockerfiles - -[:octocat: GitHub](https://github.com/Niema-Docker) - -[:whale: Docker hub](https://hub.docker.com/u/niemasd) - -Slim bioinformatics images based on Alpine Linux with useful (but optional) -common combinations. - -### Biocontainers Registry - -[:globe_with_meridians: Website](https://biocontainers.pro/) - -[:octocat: GitHub](https://github.com/BioContainers/containers) - -[:whale: Docker hub](https://hub.docker.com/u/biocontainers) - -Most of these images are already in Singularity format, and there are _a lot_ of -tools for the picking here. - -### McDonnell Genome Institute - -[:octocat: GitHub](https://github.com/orgs/genome/repositories?language=dockerfile) - -[:whale: Docker hub](https://hub.docker.com/u/mgibio) - -These folks make high-quality and well-maintained images for their own and -other tools. - -## Artwork - -Artwork was designed by [@MillironX] by remixing: - -- [DNA] by Scout (Public domain) -- [Cardboard box] by Rushtini (Public domain) -- [Pointing Boy in Baseball Cap] by ruthirsty (Public domain) -- [Singularity Logo] by Sylabs (BSD 3-Clause) - -[Nextflow]: https://nextflow.io -[Singularity]: https://sylabs.io/singularity -[Sylabs Cloud Library]: https://cloud.sylabs.io/library/millironx/default -[Install Singularity]: https://sylabs.io/guides/3.8/admin-guide/installation.html -[@MillironX]: https://github.com/MillironX -[DNA]: https://openclipart.org/detail/192915/dna -[Cardboard box]: https://openclipart.org/detail/192915/dna -[Pointing Boy in Baseball Cap]: https://openclipart.org/detail/281363/pointing-boy-in-baseball-cap -[Singularity Logo]: https://github.com/sylabs/singularity/blob/master/docs/logos/singularity_v3.svg +- `read_analysis.py` +- `simulator.py`