Merge branch 'refactor/miniforge' into dev

conda/conda.yml

@@ -13,67 +13,66 @@
         name: python3-pip
         state: latest
 
-- name: Download Miniconda
+- name: Download Miniforge
   get_url:
-        url: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-        dest: /tmp/miniconda.sh
+    url: https://github.com/conda-forge/miniforge/releases/download/{{conda_vars.MINI_FORGE_RELEASE}}/Miniforge3-{{conda_vars.MINI_FORGE_RELEASE}}-Linux-x86_64.sh
+    dest: /tmp/miniforge.sh
 
-- name: Install Miniconda
-  command: bash /tmp/miniconda.sh -b -p {{conda_vars.CONDA_DIR}}
+- name: Install Miniforge
+  command: bash /tmp/miniforge.sh -b -p {{ conda_vars.CONDA_DIR }}
   args:
-        creates: "{{conda_vars.CONDA_DIR}}/bin/conda"
+    creates: "{{ conda_vars.CONDA_DIR }}/bin/mamba"
 
-- name: Add Miniconda to PATH
+- name: Add Miniforge to PATH
   lineinfile:
-        path: /etc/profile
-        line: 'export PATH={{conda_vars.CONDA_DIR}}/bin:$PATH'
+    path: /etc/profile
+    line: 'export PATH={{ conda_vars.CONDA_DIR }}/bin:$PATH'
   become: true
   become_user: root
 
 - name: Install conda-env role
   include_role:
-        name: andrewrothstein.conda-env
+    name: andrewrothstein.conda-env
   vars:
-        conda_env_conda_dir: "{{conda_vars.CONDA_DIR}}"
-        conda_env_name: "{{ conda_vars.ENV_NAME| quote }}"
-        conda_env_environment: conda_env.yml
-        conda_env_activate_for_login_shell: true
+    conda_env_conda_dir: "{{conda_vars.CONDA_DIR}}"
+    conda_env_name: "{{ conda_vars.ENV_NAME| quote }}"
+    conda_env_environment: conda_env.yml
+    conda_env_activate_for_login_shell: true
 
-- name: Adjust miniconda folder rights
+- name: Adjust miniforge folder rights
   become: true
   shell: chown -R {{conda_vars.default_user}}:{{conda_vars.default_user}} {{conda_vars.CONDA_DIR}}/
 
 - name: Add bioconda channel
   become_user: "{{conda_vars.default_user}}"
   shell: 'timeout 1m bash -c ''source {{conda_vars.CONDA_DIR}}/bin/activate && conda config --add channels bioconda'''
   args:
-        executable: /bin/bash
+    executable: /bin/bash
 
 - name: Add conda-forge channel
   become_user: "{{conda_vars.default_user}}"
   shell: 'timeout 1m bash -c ''source {{conda_vars.CONDA_DIR}}/bin/activate && conda config --add channels conda-forge'''
   args:
-        executable: /bin/bash
-
+    executable: /bin/bash
 
 - name: Init .bashrc for conda
   become_user: "{{conda_vars.default_user}}"
   shell: 'timeout 1m bash -c ''source {{ conda_vars.CONDA_DIR}}/bin/activate && conda init'''
   args:
-        executable: /bin/bash
+    executable: /bin/bash
 
 - name: Create alias for environment
   become_user: "{{conda_vars.default_user}}"
   lineinfile:
-        path: "/home/{{conda_vars.default_user}}/.bashrc"
-        line: "alias {{conda_vars.ENV_NAME|quote}}='conda activate {{conda_vars.ENV_NAME|quote}}'"
+    path: "/home/{{conda_vars.default_user}}/.bashrc"
+    line: "alias {{conda_vars.ENV_NAME|quote}}='conda activate {{conda_vars.ENV_NAME|quote}}'"
 
 - name: Check for installed packages
   become_user: "{{conda_vars.default_user}}"
   shell: 'source {{conda_vars.CONDA_DIR}}/bin/activate && conda activate {{conda_vars.ENV_NAME|quote}} && conda list'
   register: added_packages
   args:
-        executable: /bin/bash
+    executable: /bin/bash
 
 - name: Install chosen packages
   become_user: "{{conda_vars.default_user}}"
@@ -82,6 +81,6 @@
     conda activate {{conda_vars.ENV_NAME|quote}} &&
     conda install --yes {{item.key}}={{item.value.version}}
   args:
-        executable: /bin/bash
+    executable: /bin/bash
   loop: "{{ q('dict', conda_vars.packages) }}"
   when: added_packages.stdout.find(item.key) == -1

conda/conda_env.yml

@@ -2,3 +2,4 @@
 channels:
   - conda-forge
   - bioconda
+

conda/conda_vars_file.yml

@@ -1,7 +1,8 @@
 ---
 conda_vars:
   default_user: ubuntu
-  CONDA_DIR: /home/ubuntu/miniconda3
+  CONDA_DIR: /home/ubuntu/miniforge
   ENV_NAME: denbi
   TIMEOUT_LENGTH: 5m
+  MINI_FORGE_RELEASE: 24.11.2-1
   packages:

packer/networks.json

@@ -6,6 +6,6 @@
   "dsi_production": "c174e49a-3434-410e-9e83-6175f51658b0",
   "dkfz_staging": "6f6ad650-85d6-4a22-b362-849cd2ec2364",
   "dkfz_production": "9b35565f-cec0-4f59-9228-9f4a10cee53b",
-  "berlin_staging": "    f979333a-1484-4059-874a-0966a42e505b"
+  "berlin_staging": "f979333a-1484-4059-874a-0966a42e505b"
 
 }