diff --git a/host_vars/deploy/main.yml b/host_vars/deploy/main.yml index be9db423..e2ba49e5 100644 --- a/host_vars/deploy/main.yml +++ b/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_venv: "{{ anaconda_path }}/envs/{{ NGI_venv_name }}" ngi_pipeline_conf: "{{ root_path }}/conf/" ngi_resources: "{{ root_path }}/resources/" diff --git a/install.yml b/install.yml index ce3d0cbb..dea1e371 100644 --- a/install.yml +++ b/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 } diff --git a/roles/anaconda/defaults/main.yml b/roles/anaconda/defaults/main.yml index 4a52e263..d9c9cfc0 100644 --- a/roles/anaconda/defaults/main.yml +++ b/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 }}" \ No newline at end of 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 }}" diff --git a/roles/anaconda/tasks/main.yml b/roles/anaconda/tasks/main.yml index 3305f241..d801f7ba 100644 --- a/roles/anaconda/tasks/main.yml +++ b/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" diff --git a/roles/archive-upload-ws/tasks/1_install.yml b/roles/archive-upload-ws/tasks/1_install.yml index c6410362..e06e72b1 100644 --- a/roles/archive-upload-ws/tasks/1_install.yml +++ b/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 }}" diff --git a/roles/arteria-checksum-ws/tasks/1_install.yml b/roles/arteria-checksum-ws/tasks/1_install.yml index b9208a74..b3dacf20 100644 --- a/roles/arteria-checksum-ws/tasks/1_install.yml +++ b/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 }}" diff --git a/roles/delivery/defaults/main.yml b/roles/delivery/defaults/main.yml deleted file mode 100644 index c16e53e9..00000000 --- a/roles/delivery/defaults/main.yml +++ /dev/null @@ -1,6 +0,0 @@ -delivery_env_name: "ugc_delivery_script" -delivery_env_path: "{{ sw_path }}/anaconda/envs/{{ delivery_env_name }}" - -delivery_repo: "http://github.com/molmed/delivery.git" -delivery_version: "master" -delivery_dest: "{{ sw_path }}/ugc_delivery_src" diff --git a/roles/delivery/meta/main.yml b/roles/delivery/meta/main.yml deleted file mode 100644 index 3a512133..00000000 --- a/roles/delivery/meta/main.yml +++ /dev/null @@ -1,3 +0,0 @@ -dependencies: - - { role: anaconda, tags: anaconda } - - { role: setup_base_config, tags: setup_base_config } diff --git a/roles/delivery/tasks/main.yml b/roles/delivery/tasks/main.yml deleted file mode 100644 index 0e6f263e..00000000 --- a/roles/delivery/tasks/main.yml +++ /dev/null @@ -1,44 +0,0 @@ -- name: create virtual python env for delivery - shell: conda create --name {{ delivery_env_name }} python=2.7 - args: - creates: "{{ delivery_env_path }}" - -- name: get delivery from git - git: - repo: "{{ delivery_repo }}" - dest: "{{ delivery_dest }}" - version: "{{ delivery_version }}" - -- name: install delivery requirements - pip: - executable: "{{ delivery_env_path }}/bin/pip" - requirements: "{{ delivery_dest }}/requirements.txt" - state: present - -- name: install delivery into venv - copy: - src: "{{ delivery_dest }}/deliver.py" - dest: "{{ delivery_env_path }}/bin/" - -- name: ensure conf dir exists - file: - path: "{{ ngi_pipeline_conf }}" - state: directory - -- name: deploy ugc bash env file - template: - src: sourceme_ugc.sh.j2 - dest: "{{ ngi_pipeline_conf }}/sourceme_ugc.sh" - -- name: try to get delivery commit version - command: git rev-parse HEAD - args: - chdir: "{{ delivery_dest }}" - register: delivery_version - ignore_errors: true - -- name: store delivery tool version in deployment - lineinfile: - dest: "{{ deployed_tool_versions }}" - line: "delivery: {{ delivery_version.stdout }}" - when: delivery_version.stdout diff --git a/roles/delivery/templates/sourceme_ugc.sh.j2 b/roles/delivery/templates/sourceme_ugc.sh.j2 deleted file mode 100644 index fcbaae1c..00000000 --- a/roles/delivery/templates/sourceme_ugc.sh.j2 +++ /dev/null @@ -1,4 +0,0 @@ -export PATH="{{ anaconda_env.PATH }}:$PATH" - -alias ugc-init="source activate {{ delivery_env_name }} && cd {{ delivery_env_path }}" -alias ugc-dir="cd {{ delivery_env_path }}" diff --git a/roles/nf-core/tasks/main.yml b/roles/nf-core/tasks/main.yml index 11b31045..eae36ff1 100644 --- a/roles/nf-core/tasks/main.yml +++ b/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 diff --git a/roles/ngi_pipeline/tasks/main.yml b/roles/ngi_pipeline/tasks/main.yml index 73105640..3097ddfa 100644 --- a/roles/ngi_pipeline/tasks/main.yml +++ b/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 }}"