diff --git a/README.md b/README.md index 5f467cc..9545e66 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ Tapestry is designed for manual editing of small eukaryotic genome assemblies, p ## Getting Started ### Installation -Tapestry is in the [Bioconda](https://bioconda.github.io) repository. If you are set up to use Bioconda (see [Install conda](https://bioconda.github.io/#install-conda) and [Set up channels](https://bioconda.github.io/#set-up-channels)), install the latest release with `conda`: +Tapestry is in the [Bioconda](https://bioconda.github.io) repository. If you are set up to use Bioconda (see [Install conda](https://bioconda.github.io/#install-conda) and [Set up channels](https://bioconda.github.io/#set-up-channels)), install the latest release with `conda` (or [Mamba](https://mamba.readthedocs.io/en/latest/)): ``` conda install tapestry @@ -20,21 +20,19 @@ conda install tapestry If you want to install the latest commit, make sure the requirements below are satisfied (or a previous release is installed with conda), and then pull from github and install: ``` git clone https://github.com/johnomics/tapestry -cd tapestry -python setup.py install +pip install tapestry ``` ### Requirements -Tapestry requires the following packages and tools (which will be installed by `conda` automatically): +Tapestry requires the following packages and tools: -- Linux or macOS - Python 3.6 or later - [minimap2](https://github.com/lh3/minimap2) - [samtools](http://www.htslib.org/download/) -Python packages: +Python packages (should be installed by pip): - biopython - intervaltree - jinja2 @@ -42,9 +40,10 @@ Python packages: - pandas - plumbum - pysam -- sqlalchemy +- sqlalchemy>=1.4.0 - tqdm +These dependencies can be installed with conda. Bioconda is not compatible with Apple Silicon; for recent Macs, install Python, minimap2 and samtools separately and then use `git clone` and `pip` as above. Use `make arm_neon=1` to compile minimap2 and samtools. ### Basic usage diff --git a/setup.py b/setup.py index 96bd379..1c3c968 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="tapestry", - version="1.0.0", + version="1.0.1", author="John Davey", author_email="johnomics@gmail.com", description="Validate and edit small eukaryotic genome assemblies", @@ -22,7 +22,7 @@ 'pandas', 'plumbum', 'pysam', - 'sqlalchemy', + 'sqlalchemy>=1.4.0', 'tqdm', ] ) diff --git a/tapestry/_version.py b/tapestry/_version.py index 5becc17..5c4105c 100644 --- a/tapestry/_version.py +++ b/tapestry/_version.py @@ -1 +1 @@ -__version__ = "1.0.0" +__version__ = "1.0.1"