diff --git a/README.md b/README.md index 83e090c..c7abef7 100644 --- a/README.md +++ b/README.md @@ -6,13 +6,23 @@ StxTyper is used to determine stx type from nucleotide sequence. Stx (Shiga-toxi # Installation +## Installing with Bioconda + +You'll need Mamba ([Installation instructions](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)) first. + + micromamba create -n stxtyper ncbi-stxtyper \ + --channel conda-forge \ + --channel bioconda \ + --channel defaults \ + --strict-channel-priority + ## Installing from binary ### Prerequisites #### NCBI BLAST+ -See below under "Compiling" for instructions to install. +See below under "Compiling" for instructions to install NCBI BLAST+. ### Download and install Binary @@ -24,45 +34,19 @@ Download the latest binary tarball from https://github.com/ncbi/stxtyper/release Note that we are currently only publishing binary tarballs for x86 linux. -## Installing with Bioconda - -You'll need Mamba ([Installation instructions](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)) or Conda ([Installation instructions](https://docs.anaconda.com/miniconda/miniconda-install/)) first. - - conda create -n stxtyper ncbi-stxtyper \ - --channel conda-forge \ - --channel bioconda \ - --channel defaults \ - --strict-channel-priority - -or - - micromamba create -n stxtyper ncbi-stxtyper \ - --channel conda-forge \ - --channel bioconda \ - --channel defaults \ - --strict-channel-priority - ## Compiling ### Prerequisites #### NCBI BLAST+ -StxTyper needs NCBI BLAST binaries in your path (specifically tblastn). If you don't -already have BLAST installed see https://www.ncbi.nlm.nih.gov/books/NBK569861/ -for instructions to install BLAST binaries. - -Blast can also be installed using bioconda by first installing bioconda, then making sure to activate the environment in which it's installed. -- See the [official install miniconda instructions for Linux](https://docs.anaconda.com/free/miniconda/#quick-command-line-install) -- See the [official install miniconda instructions for MacOS](https://docs.conda.io/en/latest/miniconda.html) - -Then run: - - source ~/miniconda3/bin/activate - conda create -y -c conda-forge -c bioconda -n blast blast - conda activate blast +StxTyper needs NCBI BLAST binaries in your path (specifically tblastn). If you +don't already have BLAST installed see +https://www.ncbi.nlm.nih.gov/books/NBK569861/ for the official instructions to +install BLAST binaries. It's also available in many package repositories, for +example on Ubuntu: -If you install BLAST via conda in this way you will need to run `conda activate blast` before you can run StxTyper. + sudo apt-get install ncbi-blast+ #### C compiler and make