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WardDeb merged 1 commit into from
Sep 26, 2026
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docs: step by step in docs points to zenodo files, osx install instructions simplified #1482

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2 changes: 1 addition & 1 deletion docs/content/example_step_by_step.rst
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Expand Up @@ -9,7 +9,7 @@ If you're using the command-line version you can easily follow the given example

All protocols assume that you have uploaded your files into a Galaxy instance with a deepTools installation, e.g., `deepTools Galaxy <http://deeptools.ie-freiburg.mpg.de>`_. If you need help to get started with Galaxy in general, e.g. to upload your data, see :doc:`help_galaxy_intro` and :doc:`help_galaxy_dataup`.

.. tip:: If you would like to try out the protocols with **sample data**, go to `deepTools Galaxy <http://deeptools.ie-freiburg.mpg.de>`__ --> "Shared Data" --> "Data Libraries" --> "deepTools Test Files". Simply select BED/BAM/bigWig files and click, "to History". You can also download the test data sets to your computer by clicking "Download" at the top.
.. tip:: If you would like to try out the protocols with **sample data**, test data can be downloaded from `Zenodo <https://zenodo.org/records/21529137>`__.

.. contents:: How to do...?
:local:
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8 changes: 1 addition & 7 deletions docs/content/installation.rst
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Expand Up @@ -4,7 +4,7 @@ Installation
Remember -- deepTools are available for **command line usage** as well as for
**integration into Galaxy servers** !

.. contents::
.. contents::
:local:

Command line installation using ``conda``
Expand All @@ -16,12 +16,6 @@ The recommended way to install deepTools (including its requirements) is via `mi

$ conda install -c conda-forge -c bioconda deeptools

Note that for ARM architecture (e.g. M1 on OSX) you could go via the pip installation (see below), or install via the osx-64 env:

.. code:: bash

$ CONDA_SUBDIR=osx-64 conda create -c conda-forge -c bioconda -n deeptools deeptools


Command line installation using ``pip``
---------------------------------------
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