zavolanlab · deliaBlue · Sep 19, 2023 · Sep 22, 2023 · Sep 22, 2023 · Sep 22, 2023
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -24,13 +24,13 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          channel-priority: true
           activate-environment: mirflowz
-          environment-file: environment.yml
+          environment-file: install/environment.dev.yml
           auto-activate-base: false
 
-      - name: Update mirflowz env with dev packages
-        run: mamba env update -n mirflowz -f environment.dev.yml
-
       - name: display environment info
         run: |
           conda info -a
@@ -65,12 +65,9 @@ jobs:
         with:
           mamba-version: "*"
           activate-environment: mirflowz
-          environment-file: environment.yml
+          environment-file: install/environment.dev.root.yml
           auto-activate-base: false
 
-      - name: update mirflowz env with dev packages
-        run: mamba env update -n mirflowz -f environment.dev.yml
-
       - name: display environment info
         run: |
           conda info -a
@@ -86,7 +83,7 @@ jobs:
         run: bash test/test_rule_graph.sh
 
 
-  snakemake-integration-test:
+  snakemake-singularity-integration-test:
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -101,13 +98,13 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          channel-priority: true
           activate-environment: mirflowz
-          environment-file: environment.yml
+          environment-file: install/environment.root.yml
           auto-activate-base: false
 
-      - name: update mirflowz env with root packages
-        run: mamba env update -n mirflowz -f environment.root.yml
-
       - name: display environment info
         run: |
           conda info -a
@@ -116,6 +113,34 @@ jobs:
       - name: run local test with Singularity
         run: bash test/test_workflow_local_with_singularity.sh
 
+
+  snakemake-conda-integration-test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+      - name: check out repository
+        uses: actions/checkout@v4
+
+      - name: setup Conda/Mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          channel-priority: true
+          activate-environment: mirflowz
+          environment-file: install/environment.yml
+          auto-activate-base: false
+
+      - name: display environment info
+        run: |
+          conda info -a
+          conda list   
+
       - name: run local test with Conda
         run: bash test/test_workflow_local_with_conda.sh
 
@@ -135,13 +160,13 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda
+          channel-priority: true
           activate-environment: mirflowz
-          environment-file: environment.yml
+          environment-file: install/environment.dev.yml
           auto-activate-base: false
 
-      - name: update mirflowz env with dev packages
-        run: mamba env update -n mirflowz -f environment.dev.yml
-
       - name: display environment info
         run: |
           conda info -a

diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@ _MIRFLOWZ_ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs.
 ## Table of Contents
 
 1. [Installation](#installation)
+    - [Requirements](#requirements)
     - [Cloning the repository](#cloning-the-repository)
-    - [Dependencies](#dependencies)
     - [Setting up the virtual environment](#setting-up-the-virtual-environment)
     - [Testing your installation](#testing-your-installation)
 2. [Usage](#usage)
@@ -23,17 +23,7 @@ _MIRFLOWZ_ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs.
 The workflow lives inside this repository and will be available for you to run
 after following the installation instructions laid out in this section.
 
-### Cloning the repository
-
-Traverse to the desired path on your file system, then clone the repository and
-change into it with:
-
-```bash
-git clone https://github.com/zavolanlab/mirflowz.git
-cd mirflowz
-```
-
-### Dependencies
+### Requirements
 
 For improved reproducibility and reusability of the workflow, as well as an
 easy means to run it on a high performance computing (HPC) cluster managed,
@@ -43,50 +33,58 @@ environments). As a consequence, running this workflow has only a few individual
 dependencies. These are managed by the package manager Conda, which 
 needs to be installed on your system before proceeding.
 
-If you do not already have Conda installed globally on your system,
-we recommend that you install [Miniconda][miniconda-installation]. For faster
-creation of the environment (and Conda environments in general), you can also
-install [Mamba][mamba] on top of Conda. In that case, replace `conda` with
-`mamba` in the commands below (particularly in `conda env create`).
+The installation requires the following:
 
-### Setting up the virtual environment
+- Linux (tested with Ubuntu `20.04` and `22.04`; macOS has not been tested yet)
+- [Conda][conda] (tested with `conda 23.1.0`)
+- [Mamba][mamba] (tested with `mamba 1.4.1`)
 
-Create and activate the environment with necessary dependencies with Conda:
+> Other versions, especially older ones, are not guaranteed to work.
 
-```bash
-conda env create -f environment.yml
-conda activate mirflowz
-```
+### Cloning the repository
 
-If you plan to run _MIRFLOWZ_ via Conda, we recommend using the following
-command for a faster environment creation, specially if you will run it on an
-HPC cluster.
+Traverse to the desired path on your file system, then clone the repository and
+change into it with:
 
 ```bash
-conda config --set channel_priority strict
+git clone https://github.com/zavolanlab/mirflowz.git
+# or git clone [email protected]:zavolanlab/mirflowz
+cd mirflowz
 ```
 
-If you plan to run _MIRFLOWZ_ via Singularity and do not already
-have it installed globally on your system, you must further update the Conda
-environment using the `environment.root.yml` with the command below.
-Mind that you must have the environment activated to update it.
+
+### Setting up the virtual environment
+
+You now need to create and activate the environment with necessary
+dependencies. For that purpose, there exist four different environment files.
+Use the decision matrix to pick the most suitable one for you:
+
+| I have root privileges on the machine/ I want to run _MIRFLOWZ_ via Singularity | I want to run pre-packaged tests | Environment file to use &emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; |
+|:---:|:---:| --- |
+| | | `install/environment.yml` |
+| :check_mark: | | `install/environment.root.yml` |
+| | :check_mark: | `install/environment.dev.yml` |
+| :check_mark: | :check_mark: | `install/environment.dev.root.yml` |
+
+To set up the environment, execute the call below, but do not forget to replace
+the placeholder `ENVIRONMENT` with the appropriate file from the table above:
 
 ```bash
-conda env update -f environment.root.yml
+mamba env create -f ENVIRONMENT
 ```
 
-> Note that you will need to have root permissions on your system to be able
-> to install Singularity. If you want to run _MIRFLOWZ_ on an HPC cluster
-> (recommended in almost all cases), ask your systems administrator about
-> Singularity.
-
-If you would like to contribute to _MIRFLOWZ_ development, you may find it 
-useful to further update your environment with the development dependencies:
+Finally, activate the Conda environment with:
 
 ```bash
-conda env update -f environment.dev.yml
+mamba activate mirflowz
 ```
+If you plan to run _MIRFLOWZ_ via Conda, we recommend using the following
+command for a faster environment creation, specially if you will run it on an
+HPC cluster.
 
+```bash
+conda config --set channel_priority strict
+```
 ### Testing your installation
 
 Several tests are provided to check the integrity of the installation. Follow

diff --git a/environment.dev.yml b/environment.dev.yml
diff --git a/environment.root.yml b/environment.root.yml
diff --git a/install/environment.dev.root.yml b/install/environment.dev.root.yml
@@ -0,0 +1,19 @@
+name: mirflowz
+channels:
+  - conda-forge
+  - bioconda
+dependencies: 
+  - coverage==7.3
+  - flake8==6.1
+  - flake8-docstrings==1.7
+  - gffutils==0.12
+  - graphviz==7.1.0
+  - mypy==1.6
+  - pylint==3.0
+  - pysam==0.22
+  - pytest==7.4
+  - pytest-cov
+  - python==3.9.16
+  - singularity>=3.5.2
+  - snakefmt
+  - snakemake==7.24.0
diff --git a/install/environment.dev.yml b/install/environment.dev.yml
@@ -0,0 +1,17 @@
+name: mirflowz
+channels:
+  - conda-forge
+  - bioconda
+dependencies: 
+  - coverage==7.3
+  - flake8==6.1
+  - flake8-docstrings==1.7
+  - gffutils==0.12
+  - mypy==1.6
+  - pylint==3.0
+  - pysam==0.22
+  - pytest==7.4
+  - pytest-cov
+  - python==3.9.16
+  - snakefmt
+  - snakemake==7.24.0
diff --git a/install/environment.root.yml b/install/environment.root.yml
@@ -0,0 +1,9 @@
+name: mirflowz
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - graphviz==7.1.0
+  - python==3.9.16
+  - snakemake==7.24.0
+  - singularity>=3.5.2
diff --git a/environment.yml → install/environment.yml b/environment.yml → install/environment.yml
@@ -3,6 +3,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - graphviz=7.1.0
-  - python=3.9.16
-  - snakemake=7.24.0
+  - graphviz==7.1.0
+  - python==3.9.16
+  - snakemake==7.24.0
diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml
@@ -4,4 +4,4 @@ channels:
   - bioconda
 dependencies:
   - samtools=1.16.1
-...
+...