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Added instructions for binary install
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evolarjun committed Aug 7, 2024
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Expand Up @@ -8,11 +8,6 @@ StxTyper is used to determine stx type from nucleotide sequence. Stx (shiga-toxi

## Prerequisites

### C compiler and make

These generally come standard for unix systems, if not the user will need to intall make
and GCC. MacOS users will need to go to the [App store and install
Xcode](https://apps.apple.com/in/app/xcode/id497799835?mt=12).

### NCBI BLAST

Expand All @@ -32,13 +27,33 @@ Then run:

If you install BLAST via conda in this way you will need to run `conda activate blast` before you can run StxTyper.

### C compiler and make

These are necessary if compiling from source. If using the binary distribution,
or Bioconda you won't need to worry about these. They generally come standard
for unix systems, if not the user will need to intall make and GCC. MacOS users
will need to go to the [App store and install
Xcode](https://apps.apple.com/in/app/xcode/id497799835?mt=12).

## Compiling

StxTyper should compile cleanly for Mac and Linux x86 and ARM, though our official policy is we only support x86 Linux.

git clone https://github.com/evolarjun/stxtyper.git
cd stxtyper
make
make test

## Installing from binary

Download the latest binary tarball from https://github.com/ncbi/stxtyper/releases. Untar it and run the tests e.g.:

tar xvfz stxtyper_v*.tar.gz
cd stxtyper_v*/
./test_stxtyper.sh

Note that we are currently only publishing binary tarballs for x86 linux.

# Usage

stxtyper -n <assembled_nucleotide.fa> [<options>]
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