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Add option to skip transcriptome quantification

4

For those interested in only the assembled sequences, this option can substantially reduce runtime by skipping the Kallisto build transcriptome index step. Note Kallisto is still used so as to...

dcroote

Testing - CI?

1

Is there interest in setting up continuous integration for testing BraCeR output? [Travis builds can run Docker images](https://docs.travis-ci.com/user/docker/), for example, which would make implementation easier. As a first step testing...

dcroote

It would be useful to create a conda environment for BraCeR so it can be installed through bioconda. First requested in #9 .

idalind

Dockerfile needs to change Phylip download link

1

Hi, The Phylip link in the Dockerfile does not work anymore. I think it must be replaced by https://phylipweb.github.io/phylip/download/phylip-3.697.tar.gz. And I think this has been raised before, but I was...

ulyssebaruchel

Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.4 to 43.0.1. Changelog Sourced from cryptography's changelog. 43.0.1 - 2024-09-03 * Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.3.2. .. _v43-0-0: 43.0.0...

dependabot[bot]