Skip to content

Commit f109b2a

Browse files
authored
Update INSTALL.rst
Update INSTALL.rst to account for the change to pyproject.toml
1 parent ba61079 commit f109b2a

1 file changed

Lines changed: 24 additions & 19 deletions

File tree

doc/INSTALL.rst

Lines changed: 24 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -31,26 +31,38 @@ or::
3131
or 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

3838
If these options don't work, see below.
3939

4040
Conda package manager
4141
----------------------
4242

4343
This 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
4545
python libraries or system libraries are automatically installed. You
4646
can also do all your installations in seperate isolated "environments"
4747
where installing new software will not affect packages in other
4848
environments. The downside of ``conda`` installation is that if you do not
4949
already use anaconda or miniconda, you will be building a completely
5050
new 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

5668
2. 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

233238
Completely from source
234239
+++++++++++++++++++++++

0 commit comments

Comments
 (0)