3131or grab a zip of the `latest release `_ from github and unpack
3232(replace `0.5.5 ` with version number; replace ``wget `` with ``curl -O `` for OS X)::
3333
34- $ unzip 1.0.0 .zip
35- $ cd UMI-tools-1.0.0
36- $ python setup.py install --user
34+ $ unzip 1.1.6 .zip
35+ $ cd UMI-tools-1.1.6
36+ $ pip install . --user
3737
3838If these options don't work, see below.
3939
4040Conda package manager
4141----------------------
4242
4343This is the easiest way to install ``UMI-tools `` if you are already using
44- either anaconda python or miniconda: all depedencies, whether they be
44+ either anaconda python or miniconda/minimamba : all depedencies, whether they be
4545python libraries or system libraries are automatically installed. You
4646can also do all your installations in seperate isolated "environments"
4747where installing new software will not affect packages in other
4848environments. The downside of ``conda `` installation is that if you do not
4949already use anaconda or miniconda, you will be building a completely
5050new python environment, would have to reinstall all of your libraries
51- etc. You can read more ` about conda here `_.
51+ etc.
5252
53- 1. Install miniconda (if not already installed), see `conda
53+ Anaconda, the company that created the conda package manager and maintains
54+ the anaconda package registry recently made it more difficult for larger
55+ organisations to use their packages for free.
56+
57+ However, the package manager remains open-source, and the conda-forge project
58+ provides and independent ecosystem, free from any IP issues around Anaconda.
59+
60+ Installing miniforge gives you the package manager with conda-forge defaults
61+ already set.
62+
63+ You can read more `about conda here `_.
64+
65+ 1. Install minimamba from miniforge (if not already installed), see `conda
5466 installation instructions here `_.
5567
56682. Type::
@@ -203,8 +215,8 @@ Depedencies from conda/PyPI manager
203215 `master branch `_ (which should contain the lastest development
204216 version) and unpack the zip or tar and enter the directory::
205217
206- $ unzip 1.0.0 .zip
207- $ cd UMI-tools-1.0.0
218+ $ unzip 1.1.6 .zip
219+ $ cd UMI-tools-1.1.6
208220
209221 or clone the repository::
210222
@@ -215,20 +227,13 @@ Depedencies from conda/PyPI manager
215227
216228 $ pip install -r requirements.txt
217229
218- or with ``conda ``::
230+ or with ``conda ``/`` mamba `` ::
219231
220- $ conda install setuptools
221- $ conda install pandas
222- $ conda install future
223- $ conda install scipy
224- $ conda install matplotlib
225- $ conda config --add channels bioconda
226- $ conda install regex
227- $ conda install pysam
232+ $ mamba install --only-deps -c bioconda umi_tools
228233
229- 4. Install UMI-tools using the ``setup.py `` script ::
234+ 4. Install UMI-tools using the ``pip `` ::
230235
231- $ python setup.py install --user
236+ $ pip install . --user
232237
233238Completely from source
234239+++++++++++++++++++++++
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