Use Miniforge instead of regular conda

host_vars/deploy/main.yml

@@ -39,9 +39,7 @@ static_ngi_log_path: "{{ static_ngi_pipeline_path }}/log"
 ngi_softlinks: "{{ ngi_pipeline_workdir }}/softlinks"
 
 NGI_venv_name: "NGI"
-NGI_venv_py2_name: "NGI_py2"
 ngi_pipeline_venv: "{{ sw_path }}/anaconda/envs/{{ NGI_venv_name }}"
-ngi_pipeline_venv_py2: "{{ sw_path }}/anaconda/envs/{{ NGI_venv_py2_name }}"
 
 ngi_pipeline_conf: "{{ root_path }}/conf/"
 ngi_resources: "{{ root_path }}/resources/"

install.yml

@@ -95,7 +95,6 @@
     - { role: arteria-sequencing-report-ws, tags: arteria-sequencing-report }
     - { role: snpseq-metadata-service, tags: snpseq-metadata-service }
     - { role: standalone_scripts, tags: standalone_scripts }
-    - { role: delivery, tags: delivery }
     - { role: misc-tools, tags: misc-tools }
     - { role: archive-upload-ws, tags: archive-upload }
     - { role: archive-verify-ws, tags: archive-verify }

roles/anaconda/defaults/main.yml

@@ -1,4 +1,5 @@
-anaconda_file: Anaconda3-2021.05-Linux-x86_64.sh
-anaconda_checksum: 2751ab3d678ff0277ae80f9e8a74f218cfc70fe9a9cdc7bb1c137d7e47e33d53
-anaconda_url: "http://repo.anaconda.com/archive/{{ anaconda_file }}"
-anaconda_src: "/scratch/{{ anaconda_file }}"
+anaconda_version: "24.7.1-0"
+anaconda_file: "Miniforge-pypy3-{{ anaconda_version }}-Linux-x86_64.sh"
+anaconda_checksum: 538afb0f656fffcc4b4015b676fbf3905052d3817dd091e3b1043bd7f68f0de6
+anaconda_url: "https://github.com/conda-forge/miniforge/releases/download/{{ anaconda_version }}/{{ anaconda_file }}"
+anaconda_src: "/scratch/{{ anaconda_file }}"

roles/anaconda/tasks/main.yml

@@ -11,7 +11,7 @@
     creates: "{{ anaconda_path }}/LICENSE.txt"
 
 - name: Update anaconda
-  shell: "{{ anaconda_path }}/bin/conda update -n base -c defaults conda -y"
+  shell: "{{ anaconda_path }}/bin/conda update -n base -c conda-forge conda -y"
 
 - name: "Check if {{ conda_tools_env }} virtual env exists"
   shell: "{{ anaconda_path }}/bin/conda env list"

roles/archive-upload-ws/tasks/1_install.yml

@@ -5,6 +5,9 @@
   args: 
     creates: "{{ arteria_service_env_root }}"
 
+- name: make sure pip is up to date
+  shell: "{{ arteria_service_env_root }}/bin/python -m ensurepip --upgrade"
+
 - name: get archive-upload from git
   git:
     repo: "{{ archive_upload_repo }}"

roles/arteria-checksum-ws/tasks/1_install.yml

@@ -2,9 +2,12 @@
 
 - name: create virtual python env for arteria-checksum
   shell: "conda create --name {{ arteria_service_name }} python=2.7"
-  args: 
+  args:
     creates: "{{ arteria_service_env_root }}"
 
+- name: make sure pip is up to date
+  shell: "{{ arteria_service_env_root }}/bin/python -m ensurepip --upgrade"
+
 - name: get arteria-checksum from git
   git:
     repo: "{{ arteria_checksum_repo }}"

roles/nf-core/tasks/main.yml

@@ -4,7 +4,7 @@
   register: "nfcore_envs"
 
 - name: Setup {{ nf_core_env_name }} virtual env with python3 and nf-core v{{ nf_core_version }}
-  command: "conda create -n {{ nf_core_env_name }} -c conda-forge -c bioconda -c anaconda python={{ python3_version }} nf-core={{ nf_core_version }} nextflow={{ nextflow_version_tag }} awscli={{ awscli_version }}"
+  command: "conda create -n {{ nf_core_env_name }} -c conda-forge -c bioconda python={{ python3_version }} nf-core={{ nf_core_version }} nextflow={{ nextflow_version_tag }} awscli={{ awscli_version }}"
   when: not nf_core_env_name in nfcore_envs.stdout|split
 
 # Setup pipelines

roles/ngi_pipeline/tasks/main.yml

@@ -8,10 +8,6 @@
   shell: "conda create -n {{ NGI_venv_name }} pip python={{ python3_version }}"
   when: not NGI_venv_name in py_venv_exists.stdout|split
 
-- name: Setup virtual env with python{{ python2_version }} and install dependencies
-  shell: "conda create -n {{ NGI_venv_py2_name }} -c anaconda python={{ python2_version }}"
-  when: not NGI_venv_py2_name in py_venv_exists.stdout|split
-
 - name: Fetch ngi_pipeline from github
   git:
     repo: "{{ ngi_pipeline_repo }}"