updating the docs: Depencencies.md

docs/2_Install/Dependencies.md

@@ -11,39 +11,21 @@
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-Cactus was built with the goal to make the installation as pain-free as possible. This was achieved by using only tools within containers or virtual environments for all analysis. Installation of most tools is done automatically the first time the pipeline is run. However, two key dependencies should still be installed. These are:
+Cactus was built with the goal to make the installation as pain-free as possible. This was achieved by using only tools within containers or virtual environments for all analysis. Installation of most tools is done automatically the first time the pipeline is run. However, two key dependencies should still be installed: [Nextflow](https://doi.org/10.1038/nbt.3820), and a package manager; one of these tools: [SingularityCE](https://doi.org/10.1371/journal.pone.0177459), [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241), [conda](https://docs.anaconda.com/anaconda/reference/release-notes/) and [Mamba](https://medium.com/@QuantStack/open-software-packaging-for-science-61cecee7fc23). Among these, Singularity is the recommended package manager to use if possible.
 
-1. The workflow language [Nextflow](https://doi.org/10.1038/nbt.3820) ([Install](https://www.nextflow.io/docs/latest/getstarted.html#installation)).
-Note that Cactus is currently written in DSL1, which is not supported by the latest default versions of Nextflow. Cactus users should use Nextflow version 22.10.X or earlier, such as v22.10.8 released on April 15 2023. This can be achieved with these commands:
+The current stable release of Cactus (v0.8.4) was developed and tested using these versions of the dependencies:
+ - Nextflow: 22.10.8.5859
+ - SingularityCE: 3.11.3-focal
+ - Docker: 20.10.21-0ubuntu1~20.04.2
+ - conda/Mamba: currently, running Cactus using conda or Mamba is not possible due to a [conda bug](https://github.com/conda/conda/issues/12786). 
 
+In case of issues with running Cactus, please make sure you are using the same version of the dependencies.
+
+You can find here installation links for: [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation), [SingularityCE](https://docs.sylabs.io/guides/latest/admin-guide/installation.html), [Docker](https://docs.docker.com/get-docker/), [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) and [Mamba](https://mamba.readthedocs.io/en/latest/installation.html).
+
+Please, note that Cactus is currently written in DSL1, which is [not supported anymore](https://nextflow.io/podcast/2023/ep9_end_of_dsl1_chatting_to_bots.html) by the latest default versions of Nextflow. For now, Cactus users should use Nextflow version 22.10.X or earlier, such as v22.10.8 released on April 15 2023. This can be achieved with these commands:
 ```
 wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v22.10.8/nextflow-22.10.8-all | bash
 chmod +x nextflow
 sudo mv nextflow /usr/local/bin
 ```
-
-2. A tools manager that can be any of:
- - [SingularityCE](https://doi.org/10.1371/journal.pone.0177459) ([Install](https://docs.sylabs.io/guides/latest/admin-guide/installation.html))
- - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) ([Install](https://docs.docker.com/get-docker/))
- - [conda](https://docs.anaconda.com/anaconda/reference/release-notes/) ([Install](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html))
- - [Mamba](https://medium.com/@QuantStack/open-software-packaging-for-science-61cecee7fc23) ([Install](https://mamba.readthedocs.io/en/latest/installation.html))
-
-When using conda or mamba, the set-up should be as described in [Bioconda's usage section](https://bioconda.github.io/#usage):
-```
-conda config --add channels defaults
-conda config --add channels bioconda
-conda config --add channels conda-forge
-conda config --set channel_priority strict
-```
-
-
-The current stable release of Cactus (v0.8.4) was tested using these versions of the dependencies:
-  - Nextflow: 22.10.8.5859
-
-  - SingularityCE: 3.11.3-focal
-  - Conda: 23.3.1
-  - Mamba 1.1.0 (conda 23.3.1)
-  - Docker: 20.10.21-0ubuntu1~20.04.2
-
-In case of issues with running Cactus, please make sure you are using the same version of the dependencies.
-