bioconda-recipes

Conda recipes for the bioconda channel. (by bioconda)

Bioconda-recipes Alternatives

Similar projects and alternatives to bioconda-recipes

  1. Nim

    Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).

  2. Stream

    Stream - Scalable APIs for Chat, Feeds, Moderation, & Video. Stream helps developers build engaging apps that scale to millions with performant and flexible Chat, Feeds, Moderation, and Video APIs and SDKs powered by a global edge network and enterprise-grade infrastructure.

    Stream logo
  3. pyenv

    Simple Python version management

  4. Biopython

    Official git repository for Biopython (originally converted from CVS)

  5. pyenv-virtualenv

    a pyenv plugin to manage virtualenv (a.k.a. python-virtualenv)

  6. poly

    A Go package for engineering organisms.

  7. seq

    Discontinued A high-performance, Pythonic language for bioinformatics

  8. adam

    ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

  9. InfluxDB

    InfluxDB – Built for High-Performance Time Series Workloads. InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.

    InfluxDB logo
  10. serratus

    4 bioconda-recipes VS serratus

    Ultra-deep search for novel viruses

  11. Hail

    Cloud-native genomic dataframes and batch computing

  12. seq-genomics

    Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang

  13. TeamTeri

    Bioinformatics on GCP, AWS or Azure

  14. rsmpi

    MPI bindings for Rust

  15. smk-simple-slurm

    A simple Snakemake profile for Slurm without --cluster-config

  16. ptti

    3 bioconda-recipes VS ptti

    Population-wide Testing, Tracing and Isolation Models

  17. pyenv-virtualenvwrapper

    an alternative approach to manage virtualenvs from pyenv.

  18. nimconf2021

    Slides for Nimconf21

  19. salmon

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment (by COMBINE-lab)

  20. SaaSHub

    SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

    SaaSHub logo
NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better bioconda-recipes alternative or higher similarity.

bioconda-recipes discussion

Log in or Post with

bioconda-recipes reviews and mentions

Posts with mentions or reviews of bioconda-recipes. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-02-24.
  • Azure has broken bioconda CI for 10 days running
    1 project | news.ycombinator.com | 20 May 2024
  • Why should academic researchers use Rust?
    3 projects | /r/rust | 24 Feb 2023
    Rust makes distribution and maintenance near trivial. My lab develops a fairly widely-used tool, salmon, for the quantification of transcript expression from RNA-seq data. This tool is written in C++14, and has a substantial number of dependencies. The process of updating the tool (e.g. bumping dependencies) and cutting a new release is painful. To maintain widespread availability, we distribute this tool using bioconda which uses it's own CI and setup to build new releases for (in our case) Linux and MacOS. Things break all the time. For example, recently, they bumped the compiler used to build packages. This changed some default "implementation defined" behavior, causing previously functioning code to fail. We didn't find this locally, because we didn't test that specific compiler version. When we tried to release a new version, we had to go back and fix things etc. This is not just because different compilers exist, but because the C++ specification is soooo complicated and the set of undefined and implementation defined behavior is sooo broad that it's very brittle and it's easy for things to "break" via bitrot. However, the stability provided by Rust has been phenomenal so far. In our code, we only use stable Rust features, and we have benefited tremendously from the empirical guarantee that valid Rust code (except in exceptional cases like latent bugs in the language) will remain valid. While not all crates follow it religiously, there is a reasonable respect for semantic versioning. Thus, cutting a new release of one of our Rust tools is often as simple as just updating the Cargo.toml (and Cargo.lock in the case of applications), tagging a new release in GitHub, and letting the bioconda CI do it's business with the tagged artifacts. The build "scripts" are almost always trivial because the builds just work, across platforms, across CIs, etc. Now, new projects like cargo dist look like they make this process even simpler.
  • Software engineers: consider working on genomics
    6 projects | news.ycombinator.com | 19 Nov 2022
    I contribute to Nextflow core (https://nf-co.re/) It's more of a collection of pipelines than traditional software, but there are users all around the world and a good community.

    Most of the packages on bioconda (https://bioconda.github.io/) are open source. But you probably want to find a sub-field that interests you most before finding a project.

    In grad school, we also had an ex-google software engineer volunteer with us one day a week. It was very impactful for many members of the lab to learn good engineering practices, and it wasn't at all like the sentiment others in this thread are expressing where engineers were "janitors".

  • Conda's Contrasting Command Clarification
    1 project | /r/bioinformatics | 12 May 2022
    Answering this because I believe there is no way other than looking at their "build.sh" in the recipes (e.g., in the build.sh of MOSCA, you can see the symbolic link in the 7th line will be mosca.py). One thing you can do to find the main script is also to run "find ~/anaconda3 (or miniconda3) -name *name_of_the_tool*" to find most of their scripts.
  • How to mix separated versions of Python in the cleanest way
    4 projects | /r/devops | 25 Sep 2021
    In my world (research science) we usually use anaconda, which is just a slightly higher-level wrapper around python virtual envs. But they also maintain more repositories of various modules that scientists need. e.g. https://bioconda.github.io/
  • Seq: A programming language for high-performance computational genomics
    9 projects | news.ycombinator.com | 15 Sep 2021
    Seems like there's a conda packaging on the works: https://github.com/bioconda/bioconda-recipes/pull/29660
  • A note from our sponsor - SaaSHub
    www.saashub.com | 16 Jul 2025
    SaaSHub helps you find the best software and product alternatives Learn more →

Stats

Basic bioconda-recipes repo stats
6
1,747
10.0
6 days ago

Sponsored
Stream - Scalable APIs for Chat, Feeds, Moderation, & Video.
Stream helps developers build engaging apps that scale to millions with performant and flexible Chat, Feeds, Moderation, and Video APIs and SDKs powered by a global edge network and enterprise-grade infrastructure.
getstream.io

Did you know that Shell is
the 11th most popular programming language
based on number of references?