diff --git a/.claude/skills/add-software/SKILL.md b/.claude/skills/add-software/SKILL.md index 259e543e..6e677785 100644 --- a/.claude/skills/add-software/SKILL.md +++ b/.claude/skills/add-software/SKILL.md @@ -83,7 +83,7 @@ An install runs **only when both tags are supplied**: community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install {{ version_number }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 519c22ba..52d35c3e 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -31,3 +31,17 @@ jobs: - name: ansible-lint working-directory: ansible run: uv run ansible-lint + + # ansible-lint ships no rule for this, so it needs its own gate. Facts must + # be read as ansible_facts['name']; the bare injected form is deprecated in + # ansible-core 2.21 and removed in 2.24. Covers the non-YAML templates + # (.def/.sh/.lua/.j2) that neither linter looks at. + - name: Reject bare injected facts + working-directory: ansible + run: | + if grep -rnE '\bansible_(env|processor_vcpus|processor_count|architecture)\b' \ + --include='*.yml' --include='*.yaml' --include='*.def' \ + --include='*.j2' --include='*.lua' --include='*.sh' .; then + echo "::error::Use ansible_facts['name'] - top-level fact injection is removed in ansible-core 2.24" + exit 1 + fi diff --git a/CLAUDE.md b/CLAUDE.md index 7d851f09..cf7d044b 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -89,3 +89,8 @@ uv run ansible-lint # target profile: production `vars:` must be a **mapping, not a list**. - Unpack into **`/dev/shm`**; use **`creates:`** on build commands for idempotency. - Keep any Jinja template at the **end** of a task `name:`. +- **Facts via `ansible_facts['name']`**, never the bare injected `ansible_processor_vcpus` + / `ansible_env` form — top-level injection is deprecated in ansible-core 2.21 and removed + in 2.24. `ansible.cfg` sets `inject_facts_as_vars = False`, so a bare reference fails at + runtime; a CI grep step gates it at PR time (ansible-lint has no rule for this). Magic and + connection vars (`ansible_run_tags`, `ansible_connection`) are unaffected. diff --git a/ansible/ansible.cfg b/ansible/ansible.cfg index d4b96478..6f60cfde 100644 --- a/ansible/ansible.cfg +++ b/ansible/ansible.cfg @@ -3,6 +3,10 @@ ansible_connection = ssh inventory = ./inventory roles_path = ./roles gathering = smart +# Facts are consumed via ansible_facts['name']; top-level injection is removed +# in ansible-core 2.24. Disabling it now makes any missed bare `ansible_*` +# reference fail loudly instead of silently resolving to the wrong thing. +inject_facts_as_vars = False # fact_caching = redis diff --git a/ansible/group_vars/all b/ansible/group_vars/all index 7acd9982..fee5db53 100644 --- a/ansible/group_vars/all +++ b/ansible/group_vars/all @@ -28,7 +28,7 @@ python_dir: "{{ common_dir }}/python" uv_version: "0.11.23" uv_dir: "{{ common_dir }}/uv" uv: "{{ uv_dir }}/{{ uv_version }}/bin/uv" -uv_arch: "{{ ansible_architecture }}" # x86_64 / aarch64 +uv_arch: "{{ ansible_facts['architecture'] }}" # x86_64 / aarch64 uv_checksums: x86_64: "sha256:e12c4cda2fe8c305510a78380a88f2c32a27e90cdcd123cefd2873388f0ebb5f" aarch64: "sha256:1873a77350f6621279ae1a0d2227f2bd8b67131598f14a7eb0ba2215d3da2c98" diff --git a/ansible/roles/compiled/tasks/astro/calceph.yaml b/ansible/roles/compiled/tasks/astro/calceph.yaml index 9652bde5..b177c3b9 100644 --- a/ansible/roles/compiled/tasks/astro/calceph.yaml +++ b/ansible/roles/compiled/tasks/astro/calceph.yaml @@ -1,7 +1,7 @@ --- - name: Install calceph environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" FFLAGS: "-fallow-argument-mismatch" CC: "gcc-10" FC: "gfortran-10" diff --git a/ansible/roles/compiled/tasks/astro/cfitsio.yaml b/ansible/roles/compiled/tasks/astro/cfitsio.yaml index 6fe8cc9b..318a1e9c 100644 --- a/ansible/roles/compiled/tasks/astro/cfitsio.yaml +++ b/ansible/roles/compiled/tasks/astro/cfitsio.yaml @@ -33,7 +33,7 @@ community.general.make: chdir: "{{ unzipdir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Build cfitsio shared {{ version_number }} when: "'3.' in version_number" @@ -41,7 +41,7 @@ chdir: "{{ unzipdir }}" target: shared environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install cfitsio {{ version_number }} community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/ambertools.yaml b/ansible/roles/compiled/tasks/bio/ambertools.yaml index 813a6bb4..7070d42f 100644 --- a/ansible/roles/compiled/tasks/bio/ambertools.yaml +++ b/ansible/roles/compiled/tasks/bio/ambertools.yaml @@ -22,14 +22,14 @@ - never - ambertools{{ item.version_number }} environment: - PATH: "{{ cuda_root }}/bin:{{ mpi_root }}/bin:{{ hwloc_root }}/bin:{{ python_root }}/bin:{{ ansible_env.PATH }}" - INCLUDE: "{{ cuda_root }}/include:{{ mpi_root }}/include:{{ hwloc_root }}/include:{{ python_root }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE + PATH: "{{ cuda_root }}/bin:{{ mpi_root }}/bin:{{ hwloc_root }}/bin:{{ python_root }}/bin:{{ ansible_facts['env'].PATH }}" + INCLUDE: "{{ cuda_root }}/include:{{ mpi_root }}/include:{{ hwloc_root }}/include:{{ python_root }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" - LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ mpi_root }}/lib:{{ hwloc_root }}/lib:{{ python_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH + LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ mpi_root }}/lib:{{ hwloc_root }}/lib:{{ python_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" PKG_CONFIG_PATH: "{{ cuda_root }}/pkgconfig:{{ mpi_root }}/lib/pkgconfig:{{ hwloc_root }}/lib/pkgconfig:{{ python_root }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' - in ansible_env %}:{{ ansible_env.PKG_CONFIG_PATH }}{% endif %}" - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + in ansible_facts['env'] %}:{{ ansible_facts['env'].PKG_CONFIG_PATH }}{% endif %}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" CUDA_PATH: "{{ cuda_root }}" CUDA_DIR: "{{ cuda_root }}" block: diff --git a/ansible/roles/compiled/tasks/bio/bamtools.yaml b/ansible/roles/compiled/tasks/bio/bamtools.yaml index 49fb01a6..bd5178f6 100644 --- a/ansible/roles/compiled/tasks/bio/bamtools.yaml +++ b/ansible/roles/compiled/tasks/bio/bamtools.yaml @@ -48,11 +48,11 @@ community.general.make: chdir: "{{ unzip_dir }}/build" target: all - jobs: "{{ ansible_processor_count }}" + jobs: "{{ ansible_facts['processor_count'] }}" params: DESTDIR: "{{ unzip_dir }}/staging" environment: - MAKEFLAGS: "-j {{ ansible_processor_count }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_count'] }}" - name: Run make install community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/bcftools.yaml b/ansible/roles/compiled/tasks/bio/bcftools.yaml index 6258f613..6cb57d21 100644 --- a/ansible/roles/compiled/tasks/bio/bcftools.yaml +++ b/ansible/roles/compiled/tasks/bio/bcftools.yaml @@ -39,7 +39,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install bcftools {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/beagle.yaml b/ansible/roles/compiled/tasks/bio/beagle.yaml index 56f9d734..a8d0808a 100644 --- a/ansible/roles/compiled/tasks/bio/beagle.yaml +++ b/ansible/roles/compiled/tasks/bio/beagle.yaml @@ -39,12 +39,12 @@ chdir: "{{ unzipdir }}" creates: "{{ unzipdir }}/configure" environment: - # PATH: "{{ cuda_location }}/bin:{{ ansible_env.PATH }}" - # LD_LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - # LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_env.LIBRARY_PATH | default('') }}" - # INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_env.INCLUDE | default('') }}" - # C_INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_env.C_INCLUDE | default('') }}" - # PKG_CONFIG_PATH: "{{ cuda_location }}/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + # PATH: "{{ cuda_location }}/bin:{{ ansible_facts['env'].PATH }}" + # LD_LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + # LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_facts['env'].LIBRARY_PATH | default('') }}" + # INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + # C_INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_facts['env'].C_INCLUDE | default('') }}" + # PKG_CONFIG_PATH: "{{ cuda_location }}/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" CFLAGS: "-fstack-protector -Wformat" - name: Run configure BEAGLE {{ version_number }} ansible.builtin.command: "./configure --prefix={{ install_dir }} --with-cuda={{ cuda_location }} --with-jdk={{ java_location }}" @@ -56,11 +56,11 @@ JDK_HOME: "{{ java_location }}" CC: "gcc-8" CXX: "g++-8" - PATH: "{{ java_location }}/bin:{{ ansible_env.PATH }}" - # LD_LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - # LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_env.LIBRARY_PATH | default('') }}" - # INCLUDE: "{{ cuda_location }}/include:{{ ansible_env.INCLUDE | default('') }}" - # C_INCLUDE: "{{ cuda_location }}/include:{{ ansible_env.C_INCLUDE | default('') }}" + PATH: "{{ java_location }}/bin:{{ ansible_facts['env'].PATH }}" + # LD_LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + # LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_facts['env'].LIBRARY_PATH | default('') }}" + # INCLUDE: "{{ cuda_location }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + # C_INCLUDE: "{{ cuda_location }}/include:{{ ansible_facts['env'].C_INCLUDE | default('') }}" CFLAGS: "-fstack-protector -Wformat" # GCC_EXEC_PREFIX: "-8" # - name: Run cmake BEAGLE {{ version_number }} configure @@ -69,25 +69,25 @@ # chdir: "{{ build_dir }}" ## creates: "{{ build_dir }}/Makefile" # environment: - # PATH: "{{ cuda_location }}/bin:{{ ansible_env.PATH }}" - # LD_LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - # LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_env.LIBRARY_PATH | default('') }}" - # INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_env.INCLUDE | default('') }}" - # C_INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_env.C_INCLUDE | default('') }}" - # PKG_CONFIG_PATH: "{{ cuda_location }}/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + # PATH: "{{ cuda_location }}/bin:{{ ansible_facts['env'].PATH }}" + # LD_LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + # LIBRARY_PATH: "{{ cuda_location }}/lib64:{{ cuda_location }}/extras/CUPTI/lib64:{{ ansible_facts['env'].LIBRARY_PATH | default('') }}" + # INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + # C_INCLUDE: "{{ cuda_location }}/include:{{ cuda_location }}/extras/CUPTI/include:{{ ansible_facts['env'].C_INCLUDE | default('') }}" + # PKG_CONFIG_PATH: "{{ cuda_location }}/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" # CFLAGS: "-fstack-protector -Wformat" - name: Build BEAGLE {{ version_number }} community.general.make: chdir: "{{ unzipdir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" JAVA_HOME: "{{ java_location }}" JDK_HOME: "{{ java_location }}" - PATH: "{{ java_location }}/bin:{{ ansible_env.PATH }}" - # LD_LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - # LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_env.LIBRARY_PATH | default('') }}" - # INCLUDE: "{{ cuda_location }}/include:{{ ansible_env.INCLUDE | default('') }}" - # C_INCLUDE: "{{ cuda_location }}/include:{{ ansible_env.C_INCLUDE | default('') }}" + PATH: "{{ java_location }}/bin:{{ ansible_facts['env'].PATH }}" + # LD_LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + # LIBRARY_PATH: "{{ cuda_location }}/lib:{{ ansible_facts['env'].LIBRARY_PATH | default('') }}" + # INCLUDE: "{{ cuda_location }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + # C_INCLUDE: "{{ cuda_location }}/include:{{ ansible_facts['env'].C_INCLUDE | default('') }}" # GCC_EXEC_PREFIX: "-8" - name: Install BEAGLE {{ version_number }} community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/bedtools.yaml b/ansible/roles/compiled/tasks/bio/bedtools.yaml index 7b2d729e..6de1236c 100644 --- a/ansible/roles/compiled/tasks/bio/bedtools.yaml +++ b/ansible/roles/compiled/tasks/bio/bedtools.yaml @@ -35,7 +35,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Copy bedtools {{ version_number }} binaries to {{ install_dir }} ansible.builtin.copy: src: "{{ unzip_dir }}/bin/" diff --git a/ansible/roles/compiled/tasks/bio/biobambam2.yaml b/ansible/roles/compiled/tasks/bio/biobambam2.yaml index 0eec4825..5ba85198 100644 --- a/ansible/roles/compiled/tasks/bio/biobambam2.yaml +++ b/ansible/roles/compiled/tasks/bio/biobambam2.yaml @@ -56,7 +56,7 @@ community.general.make: chdir: "{{ repo_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install biobambam2 {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ repo_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/bismark.yaml b/ansible/roles/compiled/tasks/bio/bismark.yaml index 488a7757..e3b2e9e4 100644 --- a/ansible/roles/compiled/tasks/bio/bismark.yaml +++ b/ansible/roles/compiled/tasks/bio/bismark.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/Bismark-{{ version_number }}" install_dir: "{{ bismark_dir }}/{{ version_number }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - bismark{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/bowtie2.yaml b/ansible/roles/compiled/tasks/bio/bowtie2.yaml index 4b0319ee..c6f08fab 100644 --- a/ansible/roles/compiled/tasks/bio/bowtie2.yaml +++ b/ansible/roles/compiled/tasks/bio/bowtie2.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/bowtie2-{{ version_number }}-linux-x86_64" install_dir: "{{ bowtie2_dir }}/{{ version_number }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - bowtie2-{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/bwa.yaml b/ansible/roles/compiled/tasks/bio/bwa.yaml index e229b5e7..61d8f4e7 100644 --- a/ansible/roles/compiled/tasks/bio/bwa.yaml +++ b/ansible/roles/compiled/tasks/bio/bwa.yaml @@ -28,7 +28,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: "Copy bwa and bwakit to {{ install_dir }}" ansible.builtin.command: "mv {{ unzip_dir }}/bwa {{ unzip_dir }}/bwakit {{ install_dir }}" args: diff --git a/ansible/roles/compiled/tasks/bio/chopper.yaml b/ansible/roles/compiled/tasks/bio/chopper.yaml index afa7a64f..f5e0db81 100644 --- a/ansible/roles/compiled/tasks/bio/chopper.yaml +++ b/ansible/roles/compiled/tasks/bio/chopper.yaml @@ -35,7 +35,7 @@ chdir: "{{ unzipdir }}" creates: "{{ install_dir }}/bin/chopper" environment: - PATH: "{{ cargo_dir }}/bin:{{ ansible_env.PATH | default('') }}" + PATH: "{{ cargo_dir }}/bin:{{ ansible_facts['env'].PATH | default('') }}" - name: Install chopper module {{ version_number }} block: diff --git a/ansible/roles/compiled/tasks/bio/gfaffix.yaml b/ansible/roles/compiled/tasks/bio/gfaffix.yaml index 3f99323e..90f971bb 100644 --- a/ansible/roles/compiled/tasks/bio/gfaffix.yaml +++ b/ansible/roles/compiled/tasks/bio/gfaffix.yaml @@ -34,7 +34,7 @@ chdir: "{{ unzip_dir }}" creates: "{{ install_dir }}/bin/gfaffix" environment: - PATH: "{{ cargo_dir }}/bin:{{ ansible_env.PATH | default('') }}" + PATH: "{{ cargo_dir }}/bin:{{ ansible_facts['env'].PATH | default('') }}" - name: Install GFAffix module {{ version_number }} block: diff --git a/ansible/roles/compiled/tasks/bio/gfastats.yaml b/ansible/roles/compiled/tasks/bio/gfastats.yaml index d690de6b..4214826d 100644 --- a/ansible/roles/compiled/tasks/bio/gfastats.yaml +++ b/ansible/roles/compiled/tasks/bio/gfastats.yaml @@ -32,7 +32,7 @@ community.general.make: chdir: "{{ unzipdir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Ensure installation directory exists {{ install_dir }} ansible.builtin.file: path: "{{ install_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/gromacs.yaml b/ansible/roles/compiled/tasks/bio/gromacs.yaml index 984a12ba..28d757bb 100644 --- a/ansible/roles/compiled/tasks/bio/gromacs.yaml +++ b/ansible/roles/compiled/tasks/bio/gromacs.yaml @@ -19,16 +19,16 @@ - never - gromacs{{ item.version_number }} environment: - # PATH: "{{ cuda_root }}/bin:{{ mpi_root }}/bin:{{ hwloc_root }}/bin:{{ ansible_env.PATH }}" - # INCLUDE: "{{ cuda_root }}/include:{{ mpi_root }}/include:{{ hwloc_root }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE }}{% endif %}" - # LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ mpi_root }}/lib:{{ hwloc_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH }}{% endif %}" - # PKG_CONFIG_PATH: "{{ cuda_root }}/pkgconfig:{{ mpi_root }}/lib/pkgconfig:{{ hwloc_root }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_env %}:{{ ansible_env.PKG_CONFIG_PATH }}{% endif %}" - PATH: "{{ cuda_root }}/bin:{{ hwloc_root }}/bin:{{ ansible_env.PATH }}" - INCLUDE: "{{ cuda_root }}/include:{{ hwloc_root }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE }}{% endif %}" - LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ hwloc_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH }}{% endif %}" - PKG_CONFIG_PATH: "{{ cuda_root }}/pkgconfig:{{ hwloc_root }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_env %}:{{ ansible_env.PKG_CONFIG_PATH }}{% endif + # PATH: "{{ cuda_root }}/bin:{{ mpi_root }}/bin:{{ hwloc_root }}/bin:{{ ansible_facts['env'].PATH }}" + # INCLUDE: "{{ cuda_root }}/include:{{ mpi_root }}/include:{{ hwloc_root }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" + # LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ mpi_root }}/lib:{{ hwloc_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" + # PKG_CONFIG_PATH: "{{ cuda_root }}/pkgconfig:{{ mpi_root }}/lib/pkgconfig:{{ hwloc_root }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].PKG_CONFIG_PATH }}{% endif %}" + PATH: "{{ cuda_root }}/bin:{{ hwloc_root }}/bin:{{ ansible_facts['env'].PATH }}" + INCLUDE: "{{ cuda_root }}/include:{{ hwloc_root }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" + LD_LIBRARY_PATH: "{{ cuda_root }}/lib64:{{ hwloc_root }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" + PKG_CONFIG_PATH: "{{ cuda_root }}/pkgconfig:{{ hwloc_root }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].PKG_CONFIG_PATH }}{% endif %}" - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" # CMAKE_CXX_COMPILER: "{{ mpi_root }}/bin/mpicxx" block: - name: Download GROMACS {{ version_number }} diff --git a/ansible/roles/compiled/tasks/bio/hifiasm.yaml b/ansible/roles/compiled/tasks/bio/hifiasm.yaml index 7906086c..11caaa9f 100644 --- a/ansible/roles/compiled/tasks/bio/hifiasm.yaml +++ b/ansible/roles/compiled/tasks/bio/hifiasm.yaml @@ -8,7 +8,7 @@ version_number: "{{ item.version_number }}" url: "{{ item.url }}" environment: - MAKEFLAGS: "-j{{ ansible_processor_vcpus | default(1) }}" + MAKEFLAGS: "-j{{ ansible_facts['processor_vcpus'] | default(1) }}" tags: - never - hifiasm{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/htslib.yaml b/ansible/roles/compiled/tasks/bio/htslib.yaml index 2862a5bf..517a1361 100644 --- a/ansible/roles/compiled/tasks/bio/htslib.yaml +++ b/ansible/roles/compiled/tasks/bio/htslib.yaml @@ -39,7 +39,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install htslib {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/htstream.yaml b/ansible/roles/compiled/tasks/bio/htstream.yaml index 9ab358ab..eb69dddd 100644 --- a/ansible/roles/compiled/tasks/bio/htstream.yaml +++ b/ansible/roles/compiled/tasks/bio/htstream.yaml @@ -12,7 +12,7 @@ boost_dir: "{{ item.boost_dir }}" boost_module: "{{ item.boost_module }}" environment: - LD_LIBRARY_PATH: "{{ boost_dir }}/lib:{{ ansible_env.PATH }}" + LD_LIBRARY_PATH: "{{ boost_dir }}/lib:{{ ansible_facts['env'].PATH }}" INCLUDE: "{{ boost_dir }}/include" MAKEFLAGS: "-j 1" tags: diff --git a/ansible/roles/compiled/tasks/bio/hyphy.yaml b/ansible/roles/compiled/tasks/bio/hyphy.yaml index bd6f39f2..fe082bf0 100644 --- a/ansible/roles/compiled/tasks/bio/hyphy.yaml +++ b/ansible/roles/compiled/tasks/bio/hyphy.yaml @@ -39,21 +39,21 @@ args: chdir: "{{ unzip_dir }}/" environment: - PATH: "{{ mpi_dir }}/bin:{{ ansible_env.PATH }}" - LD_LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ mpi_dir }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ mpi_dir }}/include:{{ ansible_env.INCLUDE | default('') }}" + PATH: "{{ mpi_dir }}/bin:{{ ansible_facts['env'].PATH }}" + LD_LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ mpi_dir }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ mpi_dir }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" - name: Make hyphy MPI {{ version_number }} community.general.make: chdir: "{{ unzip_dir }}" target: HYPHYMPI environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" - LD_LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ mpi_dir }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ mpi_dir }}/include:{{ ansible_env.INCLUDE | default('') }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" + LD_LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ mpi_dir }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ mpi_dir }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ mpi_dir }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" - name: Install hyphy {{ version_number }} community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/indelible.yaml b/ansible/roles/compiled/tasks/bio/indelible.yaml index 3badadbe..9f5cea92 100644 --- a/ansible/roles/compiled/tasks/bio/indelible.yaml +++ b/ansible/roles/compiled/tasks/bio/indelible.yaml @@ -28,7 +28,7 @@ - indelible{{ item.version_number }} environment: PATH: "{{ bwa_location }}:{{ samtools_location }}/bin:{{ htslib_location }}/bin:{{ bcftools_location }}/bin:{{ bedtools_location }}:{{ blast_location }}/bin:{{ - python_location }}/bin:{{ ansible_env.PATH }}" + python_location }}/bin:{{ ansible_facts['env'].PATH }}" block: - name: Create indelible directory diff --git a/ansible/roles/compiled/tasks/bio/kallisto.yaml b/ansible/roles/compiled/tasks/bio/kallisto.yaml index cac88b3e..dbe9fbd2 100644 --- a/ansible/roles/compiled/tasks/bio/kallisto.yaml +++ b/ansible/roles/compiled/tasks/bio/kallisto.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/kallisto-{{ version_number }}" install_dir: "{{ kallisto_dir }}/{{ version_number }}" # environment: - # MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + # MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - kallisto{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/libmaus2.yaml b/ansible/roles/compiled/tasks/bio/libmaus2.yaml index 30fc3dd8..8bcb1229 100644 --- a/ansible/roles/compiled/tasks/bio/libmaus2.yaml +++ b/ansible/roles/compiled/tasks/bio/libmaus2.yaml @@ -33,7 +33,7 @@ community.general.make: chdir: "{{ repo_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install libmaus2 {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ repo_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/mafft.yaml b/ansible/roles/compiled/tasks/bio/mafft.yaml index 53a06c34..52e05191 100644 --- a/ansible/roles/compiled/tasks/bio/mafft.yaml +++ b/ansible/roles/compiled/tasks/bio/mafft.yaml @@ -46,7 +46,7 @@ community.general.make: chdir: "{{ unzip_dir }}/{{ sub_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" loop: - "core" - "extensions" @@ -58,7 +58,7 @@ chdir: "{{ unzip_dir }}/{{ sub_dir }}" target: "install" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" loop: - "core" - "extensions" diff --git a/ansible/roles/compiled/tasks/bio/phyml.yaml b/ansible/roles/compiled/tasks/bio/phyml.yaml index 9f72972b..7adc658d 100644 --- a/ansible/roles/compiled/tasks/bio/phyml.yaml +++ b/ansible/roles/compiled/tasks/bio/phyml.yaml @@ -47,7 +47,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install phyml {{ version_number }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/popdel.yaml b/ansible/roles/compiled/tasks/bio/popdel.yaml index 9eee4115..653a09fe 100644 --- a/ansible/roles/compiled/tasks/bio/popdel.yaml +++ b/ansible/roles/compiled/tasks/bio/popdel.yaml @@ -37,7 +37,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" CPATH: "{{ htslib_dir }}/include" LD_LIBRARY_PATH: "{{ htslib_dir }}/lib" LIBRARY_PATH: "{{ htslib_dir }}/lib" diff --git a/ansible/roles/compiled/tasks/bio/rfmix.yaml b/ansible/roles/compiled/tasks/bio/rfmix.yaml index ae1b2de3..77a78b1f 100644 --- a/ansible/roles/compiled/tasks/bio/rfmix.yaml +++ b/ansible/roles/compiled/tasks/bio/rfmix.yaml @@ -31,7 +31,7 @@ community.general.make: chdir: "{{ bio_src }}/rfmix" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Run make install community.general.make: chdir: "{{ bio_src }}/rfmix" diff --git a/ansible/roles/compiled/tasks/bio/rsem.yaml b/ansible/roles/compiled/tasks/bio/rsem.yaml index 3c470cb6..e4bd9382 100644 --- a/ansible/roles/compiled/tasks/bio/rsem.yaml +++ b/ansible/roles/compiled/tasks/bio/rsem.yaml @@ -16,12 +16,12 @@ - never - rsem{{ item.version_number }} environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" - LD_LIBRARY_PATH: "{{ r_dir }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH }}{% endif %}" - LIBRARY_PATH: "{{ r_dir }}/lib{% if 'LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LIBRARY_PATH }}{% endif %}" - PATH: "{{ r_dir }}/bin{% if 'PATH' in ansible_env %}:{{ ansible_env.PATH }}{% endif %}" - INCLUDE: "{{ r_dir }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE }}{% endif %}" - C_INCLUDE: "{{ r_dir }}/include{% if 'C_INCLUDE' in ansible_env %}:{{ ansible_env.C_INCLUDE }}{% endif %}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" + LD_LIBRARY_PATH: "{{ r_dir }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" + LIBRARY_PATH: "{{ r_dir }}/lib{% if 'LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LIBRARY_PATH }}{% endif %}" + PATH: "{{ r_dir }}/bin{% if 'PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].PATH }}{% endif %}" + INCLUDE: "{{ r_dir }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" + C_INCLUDE: "{{ r_dir }}/include{% if 'C_INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].C_INCLUDE }}{% endif %}" block: - name: Download RSEM {{ version_number }} ansible.builtin.get_url: diff --git a/ansible/roles/compiled/tasks/bio/salmon.yaml b/ansible/roles/compiled/tasks/bio/salmon.yaml index e7754242..1862b4c7 100644 --- a/ansible/roles/compiled/tasks/bio/salmon.yaml +++ b/ansible/roles/compiled/tasks/bio/salmon.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/salmon-latest_linux_x86_64" install_dir: "{{ salmon_dir }}/{{ version_number }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - salmon{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/samtools.yaml b/ansible/roles/compiled/tasks/bio/samtools.yaml index a0c2440b..dfe1f8dc 100644 --- a/ansible/roles/compiled/tasks/bio/samtools.yaml +++ b/ansible/roles/compiled/tasks/bio/samtools.yaml @@ -39,7 +39,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install samtools {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/seqwish.yaml b/ansible/roles/compiled/tasks/bio/seqwish.yaml index 636db056..4951e975 100644 --- a/ansible/roles/compiled/tasks/bio/seqwish.yaml +++ b/ansible/roles/compiled/tasks/bio/seqwish.yaml @@ -42,24 +42,24 @@ args: chdir: "{{ bio_src }}/seqwish" environment: - LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Run cmake build - ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_processor_vcpus }}" + ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_facts['processor_vcpus'] }}" args: chdir: "{{ bio_src }}/seqwish" environment: - LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Run make install community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/smoothxg.yaml b/ansible/roles/compiled/tasks/bio/smoothxg.yaml index 9057720d..700a3134 100644 --- a/ansible/roles/compiled/tasks/bio/smoothxg.yaml +++ b/ansible/roles/compiled/tasks/bio/smoothxg.yaml @@ -43,24 +43,24 @@ args: chdir: "{{ bio_src }}/smoothxg" environment: - LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ zstd }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ zstd }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Run cmake build - ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_processor_vcpus }}" + ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_facts['processor_vcpus'] }}" args: chdir: "{{ bio_src }}/smoothxg" environment: - LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ zstd }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + LD_LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ jemalloc }}/lib:{{ zstd }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ jemalloc }}/include:{{ zstd }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ jemalloc }}/lib/pkgconfig:{{ zstd }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Copy odgi binary to install dir ansible.builtin.copy: src: "{{ bio_src }}/smoothxg/deps/odgi/bin/odgi" diff --git a/ansible/roles/compiled/tasks/bio/spliceai.yaml b/ansible/roles/compiled/tasks/bio/spliceai.yaml index 554776f0..0d48a564 100644 --- a/ansible/roles/compiled/tasks/bio/spliceai.yaml +++ b/ansible/roles/compiled/tasks/bio/spliceai.yaml @@ -10,7 +10,7 @@ - never - spliceai{{ item.version_number }} environment: - PATH: "{{ python_location }}/bin:{{ ansible_env.PATH }}" + PATH: "{{ python_location }}/bin:{{ ansible_facts['env'].PATH }}" block: - name: Create spliceai directory ansible.builtin.file: diff --git a/ansible/roles/compiled/tasks/bio/stacks.yaml b/ansible/roles/compiled/tasks/bio/stacks.yaml index 9e3988ae..befb4b21 100644 --- a/ansible/roles/compiled/tasks/bio/stacks.yaml +++ b/ansible/roles/compiled/tasks/bio/stacks.yaml @@ -40,7 +40,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install stacks {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/star.yaml b/ansible/roles/compiled/tasks/bio/star.yaml index 19646764..1524d895 100644 --- a/ansible/roles/compiled/tasks/bio/star.yaml +++ b/ansible/roles/compiled/tasks/bio/star.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/STAR-{{ version_number }}" install_dir: "{{ star_dir }}/{{ version_number }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - star{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/subread.yaml b/ansible/roles/compiled/tasks/bio/subread.yaml index 71a6e4d6..b5a5a55f 100644 --- a/ansible/roles/compiled/tasks/bio/subread.yaml +++ b/ansible/roles/compiled/tasks/bio/subread.yaml @@ -9,7 +9,7 @@ unarchive_dir: "/dev/shm/subread-{{ version_number }}-source" install_dir: "{{ subread_dir }}/{{ version_number }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - subread{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/bio/vcfbub.yaml b/ansible/roles/compiled/tasks/bio/vcfbub.yaml index 542e0396..6f6b91b7 100644 --- a/ansible/roles/compiled/tasks/bio/vcfbub.yaml +++ b/ansible/roles/compiled/tasks/bio/vcfbub.yaml @@ -28,7 +28,7 @@ chdir: "{{ bio_src }}/vcfbub" creates: "{{ install_dir }}/bin/vcfbub" environment: - PATH: "{{ cargo_dir }}/bin:{{ ansible_env.PATH | default('') }}" + PATH: "{{ cargo_dir }}/bin:{{ ansible_facts['env'].PATH | default('') }}" - name: Install vcfbub module {{ version_number }} block: diff --git a/ansible/roles/compiled/tasks/bio/vcftools.yaml b/ansible/roles/compiled/tasks/bio/vcftools.yaml index a6b6873f..1eb5fbb7 100644 --- a/ansible/roles/compiled/tasks/bio/vcftools.yaml +++ b/ansible/roles/compiled/tasks/bio/vcftools.yaml @@ -40,7 +40,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install vcftools {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/bio/vip.yaml b/ansible/roles/compiled/tasks/bio/vip.yaml index 1f76f0a9..1d20206d 100644 --- a/ansible/roles/compiled/tasks/bio/vip.yaml +++ b/ansible/roles/compiled/tasks/bio/vip.yaml @@ -12,7 +12,7 @@ - never - vip{{ item.version_number }} environment: - PATH: "/software/common/apptainer/1.4.2/bin:/software/common/java/jdk-22.0.1/bin:{{ ansible_env.PATH }}" + PATH: "/software/common/apptainer/1.4.2/bin:/software/common/java/jdk-22.0.1/bin:{{ ansible_facts['env'].PATH }}" JAVA_HOME: "/software/common/java/jdk-22.0.1" block: - name: "Download and install VIP {{ version_number }}" diff --git a/ansible/roles/compiled/tasks/bio/wfmash.yaml b/ansible/roles/compiled/tasks/bio/wfmash.yaml index a31882b3..062f7bb6 100644 --- a/ansible/roles/compiled/tasks/bio/wfmash.yaml +++ b/ansible/roles/compiled/tasks/bio/wfmash.yaml @@ -46,26 +46,26 @@ args: chdir: "{{ bio_src }}/wfmash" environment: - PATH: "{{ htslib }}/bin:{{ libgsl }}/bin:{{ ansible_env.PATH }}" - LD_LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ htslib }}/lib/pkgconfig:{{ libgsl }}/lib/pkgconfig:{{ jemalloc }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + PATH: "{{ htslib }}/bin:{{ libgsl }}/bin:{{ ansible_facts['env'].PATH }}" + LD_LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ htslib }}/lib/pkgconfig:{{ libgsl }}/lib/pkgconfig:{{ jemalloc }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Run cmake build - ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_processor_vcpus }}" + ansible.builtin.shell: "/usr/bin/cmake --build build -- -j {{ ansible_facts['processor_vcpus'] }}" args: chdir: "{{ bio_src }}/wfmash" environment: - PATH: "{{ htslib }}/bin:{{ libgsl }}/bin:{{ ansible_env.PATH }}" - LD_LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - C_INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - CPATH: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_env.INCLUDE | default('') }}" - PKG_CONFIG_PATH: "{{ htslib }}/lib/pkgconfig:{{ libgsl }}/lib/pkgconfig:{{ jemalloc }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" + PATH: "{{ htslib }}/bin:{{ libgsl }}/bin:{{ ansible_facts['env'].PATH }}" + LD_LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + LIBRARY_PATH: "{{ htslib }}/lib:{{ libgsl }}/lib:{{ jemalloc }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + C_INCLUDE: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + CPATH: "{{ htslib }}/include:{{ libgsl }}/include:{{ jemalloc }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + PKG_CONFIG_PATH: "{{ htslib }}/lib/pkgconfig:{{ libgsl }}/lib/pkgconfig:{{ jemalloc }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" - name: Run make install community.general.make: diff --git a/ansible/roles/compiled/tasks/bio/yacrd.yaml b/ansible/roles/compiled/tasks/bio/yacrd.yaml index acab1ab3..b5757509 100644 --- a/ansible/roles/compiled/tasks/bio/yacrd.yaml +++ b/ansible/roles/compiled/tasks/bio/yacrd.yaml @@ -35,7 +35,7 @@ chdir: "{{ unzipdir }}" creates: "{{ install_dir }}/bin/yacrd" environment: - PATH: "{{ cargo_dir }}/bin:{{ ansible_env.PATH | default('') }}" + PATH: "{{ cargo_dir }}/bin:{{ ansible_facts['env'].PATH | default('') }}" - name: Install yacrd module {{ version_number }} block: diff --git a/ansible/roles/compiled/tasks/common/R.yaml b/ansible/roles/compiled/tasks/common/R.yaml index b7060755..772fca81 100644 --- a/ansible/roles/compiled/tasks/common/R.yaml +++ b/ansible/roles/compiled/tasks/common/R.yaml @@ -17,13 +17,13 @@ - never - R{{ item.version_number }} environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" - LD_LIBRARY_PATH: "{{ fribidi }}/lib:{{ harfbuzz }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH }}{% endif %}" - LIBRARY_PATH: "{{ fribidi }}/lib:{{ harfbuzz }}/lib{% if 'LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LIBRARY_PATH }}{% endif %}" - PATH: "{{ fribidi }}/bin:{{ harfbuzz }}/bin:{{ install_dir }}/bin{% if 'PATH' in ansible_env %}:{{ ansible_env.PATH }}{% endif %}" - INCLUDE: "{{ fribidi }}/include:{{ harfbuzz }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE }}{% endif %}" - C_INCLUDE: "{{ fribidi }}/include:{{ harfbuzz }}/include{% if 'C_INCLUDE' in ansible_env %}:{{ ansible_env.C_INCLUDE }}{% endif %}" - PKG_CONFIG_PATH: "{{ fribidi }}/lib/pkgconfig:{{ harfbuzz }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_env %}:{{ ansible_env.PKG_CONFIG_PATH }}{% endif + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" + LD_LIBRARY_PATH: "{{ fribidi }}/lib:{{ harfbuzz }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" + LIBRARY_PATH: "{{ fribidi }}/lib:{{ harfbuzz }}/lib{% if 'LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LIBRARY_PATH }}{% endif %}" + PATH: "{{ fribidi }}/bin:{{ harfbuzz }}/bin:{{ install_dir }}/bin{% if 'PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].PATH }}{% endif %}" + INCLUDE: "{{ fribidi }}/include:{{ harfbuzz }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" + C_INCLUDE: "{{ fribidi }}/include:{{ harfbuzz }}/include{% if 'C_INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].C_INCLUDE }}{% endif %}" + PKG_CONFIG_PATH: "{{ fribidi }}/lib/pkgconfig:{{ harfbuzz }}/lib/pkgconfig{% if 'PKG_CONFIG_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].PKG_CONFIG_PATH }}{% endif %}" block: - name: Download R and install {{ version_number }} @@ -57,7 +57,7 @@ community.general.make: chdir: "{{ build_dir }}" target: install - jobs: "{{ ansible_processor_count }}" + jobs: "{{ ansible_facts['processor_count'] }}" - name: Ensure Rprofile.site is up-to-date ansible.builtin.lineinfile: path: "{{ install_dir }}/lib/R/etc/Rprofile.site" @@ -67,7 +67,7 @@ tags: Rprofile - name: Install R packages {{ r_packages }} - ansible.builtin.command: "{{ install_dir }}/bin/Rscript -e 'install.packages(c({{ r_packages }}), repos=\"http://cran.rstudio.com/\", Ncpus={{ ansible_processor_vcpus + ansible.builtin.command: "{{ install_dir }}/bin/Rscript -e 'install.packages(c({{ r_packages }}), repos=\"http://cran.rstudio.com/\", Ncpus={{ ansible_facts['processor_vcpus'] }}, user=FALSE)'" - name: Install Jupyter Kernel ansible.builtin.command: "{{ install_dir }}/bin/Rscript -e 'install.packages(\"IRkernel\", repos=\"http://cran.rstudio.com/\", user=FALSE)'" diff --git a/ansible/roles/compiled/tasks/common/apache_spark.yaml b/ansible/roles/compiled/tasks/common/apache_spark.yaml index 5916f485..5b38bdd7 100644 --- a/ansible/roles/compiled/tasks/common/apache_spark.yaml +++ b/ansible/roles/compiled/tasks/common/apache_spark.yaml @@ -41,7 +41,7 @@ # make: # chdir: "{{ build_dir }}" # environment: -# MAKEFLAGS: "-j {{ ansible_processor_count }}" +# MAKEFLAGS: "-j {{ ansible_facts['processor_count'] }}" # - name: Install OpenMPI {{ version_number }} # make: # chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/apptainer.yaml b/ansible/roles/compiled/tasks/common/apptainer.yaml index 8ad819a2..276cc879 100644 --- a/ansible/roles/compiled/tasks/common/apptainer.yaml +++ b/ansible/roles/compiled/tasks/common/apptainer.yaml @@ -13,11 +13,11 @@ squashfuse_module: "{{ item.squashfuse_module }}" gocryptfs_module: "{{ item.gocryptfs_module }}" environment: - LD_LIBRARY_PATH: "{{ squashfuse_location }}/lib:{{ gocryptfs_location }}/lib:{{ ansible_env.LD_LIBRARY_PATH | default('') }}" - PKG_CONFIG_PATH: "{{ squashfuse_location }}/lib/pkgconfig:{{ gocryptfs_location }}/lib/pkgconfig:{{ ansible_env.PKG_CONFIG_PATH | default('') }}" - INCLUDE: "{{ squashfuse_location }}/include:{{ gocryptfs_location }}/include:{{ ansible_env.INCLUDE | default('') }}" - LIBRARY_PATH: "{{ squashfuse_location }}/lib:{{ gocryptfs_location }}/lib:{{ ansible_env.LIBRARY_PATH | default('') }}" - PATH: "{{ squashfuse_location }}/bin:{{ gocryptfs_location }}/bin:{{ ansible_env.PATH }}" + LD_LIBRARY_PATH: "{{ squashfuse_location }}/lib:{{ gocryptfs_location }}/lib:{{ ansible_facts['env'].LD_LIBRARY_PATH | default('') }}" + PKG_CONFIG_PATH: "{{ squashfuse_location }}/lib/pkgconfig:{{ gocryptfs_location }}/lib/pkgconfig:{{ ansible_facts['env'].PKG_CONFIG_PATH | default('') }}" + INCLUDE: "{{ squashfuse_location }}/include:{{ gocryptfs_location }}/include:{{ ansible_facts['env'].INCLUDE | default('') }}" + LIBRARY_PATH: "{{ squashfuse_location }}/lib:{{ gocryptfs_location }}/lib:{{ ansible_facts['env'].LIBRARY_PATH | default('') }}" + PATH: "{{ squashfuse_location }}/bin:{{ gocryptfs_location }}/bin:{{ ansible_facts['env'].PATH }}" tags: - never - apptainer{{ item.version_number }} @@ -55,13 +55,13 @@ chdir: "{{ unzip_dir }}" creates: "{{ unzip_dir }}/builddir/Makefile" environment: - PATH: "{{ go_location }}:{{ ansible_env.PATH }}" + PATH: "{{ go_location }}:{{ ansible_facts['env'].PATH }}" - name: Compile apptainer community.general.make: chdir: "{{ unzip_dir }}/builddir" environment: - PATH: "{{ go_location }}:{{ ansible_env.PATH }}" - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + PATH: "{{ go_location }}:{{ ansible_facts['env'].PATH }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install apptainer community.general.make: chdir: "{{ unzip_dir }}/builddir" diff --git a/ansible/roles/compiled/tasks/common/fftw_precisions.yaml b/ansible/roles/compiled/tasks/common/fftw_precisions.yaml index 03847b97..0bd5c789 100644 --- a/ansible/roles/compiled/tasks/common/fftw_precisions.yaml +++ b/ansible/roles/compiled/tasks/common/fftw_precisions.yaml @@ -24,32 +24,32 @@ INCLUDE: "{{ mpi_dir }}/include" C_INCLUDE_PATH: "{{ mpi_dir }}/include" CPATH: "{{ mpi_dir }}/include" - PATH: "{{ mpi_dir }}/bin:{{ ansible_env.PATH }}" + PATH: "{{ mpi_dir }}/bin:{{ ansible_facts['env'].PATH }}" PKG_CONFIG_PATH: "{{ mpi_dir }}/lib/pkgconfig" - name: Build fftw {{ version_number }}-{{ name }} community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" LD_LIBRARY_PATH: "{{ mpi_dir }}/lib" LIBRARY_PATH: "{{ mpi_dir }}/lib" INCLUDE: "{{ mpi_dir }}/include" C_INCLUDE_PATH: "{{ mpi_dir }}/include" CPATH: "{{ mpi_dir }}/include" - PATH: "{{ mpi_dir }}/bin:{{ ansible_env.PATH }}" + PATH: "{{ mpi_dir }}/bin:{{ ansible_facts['env'].PATH }}" PKG_CONFIG_PATH: "{{ mpi_dir }}/lib/pkgconfig" # - name: Run make check # make: # chdir: "{{ build_dir }}" # target: check # environment: - # MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + # MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" # LD_LIBRARY_PATH: "{{ mpi_dir }}/lib" # LIBRARY_PATH: "{{ mpi_dir }}/lib" # INCLUDE: "{{ mpi_dir }}/include" # C_INCLUDE_PATH: "{{ mpi_dir }}/include" # CPATH: "{{ mpi_dir }}/include" - # PATH: "{{ mpi_dir }}/bin:{{ ansible_env.PATH }}" + # PATH: "{{ mpi_dir }}/bin:{{ ansible_facts['env'].PATH }}" # PKG_CONFIG_PATH: "{{ mpi_dir }}/lib/pkgconfig" - name: Install fftw {{ version_number }}-{{ name }} community.general.make: diff --git a/ansible/roles/compiled/tasks/common/fribidi.yaml b/ansible/roles/compiled/tasks/common/fribidi.yaml index afad29f1..dd37c154 100644 --- a/ansible/roles/compiled/tasks/common/fribidi.yaml +++ b/ansible/roles/compiled/tasks/common/fribidi.yaml @@ -13,7 +13,7 @@ - never - fribidi{{ item.version_number }} environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" block: - name: Download fribidi {{ version_number }} ansible.builtin.get_url: diff --git a/ansible/roles/compiled/tasks/common/gettext.yaml b/ansible/roles/compiled/tasks/common/gettext.yaml index 5daed419..bed5d8cf 100644 --- a/ansible/roles/compiled/tasks/common/gettext.yaml +++ b/ansible/roles/compiled/tasks/common/gettext.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install gettext {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/git.yaml b/ansible/roles/compiled/tasks/common/git.yaml index eb86d8c0..f56ed497 100644 --- a/ansible/roles/compiled/tasks/common/git.yaml +++ b/ansible/roles/compiled/tasks/common/git.yaml @@ -12,10 +12,10 @@ gettext_dir: "{{ item.gettext_dir }}" gettext_module: "{{ item.gettext_module }}" environment: - PATH: "{{ gettext_dir }}/bin:{{ ansible_env.PATH }}" - LD_LIBRARY_PATH: "{{ gettext_dir }}/lib{% if 'LD_LIBRARY_PATH' in ansible_env %}:{{ ansible_env.LD_LIBRARY_PATH }}{% endif %}" - INCLUDE: "{{ gettext_dir }}/include{% if 'INCLUDE' in ansible_env %}:{{ ansible_env.INCLUDE }}{% endif %}" - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + PATH: "{{ gettext_dir }}/bin:{{ ansible_facts['env'].PATH }}" + LD_LIBRARY_PATH: "{{ gettext_dir }}/lib{% if 'LD_LIBRARY_PATH' in ansible_facts['env'] %}:{{ ansible_facts['env'].LD_LIBRARY_PATH }}{% endif %}" + INCLUDE: "{{ gettext_dir }}/include{% if 'INCLUDE' in ansible_facts['env'] %}:{{ ansible_facts['env'].INCLUDE }}{% endif %}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" tags: - never - git{{ item.version_number }} diff --git a/ansible/roles/compiled/tasks/common/graphviz.yaml b/ansible/roles/compiled/tasks/common/graphviz.yaml index 85f27adf..c9d4d221 100644 --- a/ansible/roles/compiled/tasks/common/graphviz.yaml +++ b/ansible/roles/compiled/tasks/common/graphviz.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install graphviz {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/gsl.yaml b/ansible/roles/compiled/tasks/common/gsl.yaml index 06580e13..7a6b88f5 100644 --- a/ansible/roles/compiled/tasks/common/gsl.yaml +++ b/ansible/roles/compiled/tasks/common/gsl.yaml @@ -38,7 +38,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install Gnu Scientific Library (libgsl) {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/harfbuzz.yaml b/ansible/roles/compiled/tasks/common/harfbuzz.yaml index 350a7e83..4b606c29 100644 --- a/ansible/roles/compiled/tasks/common/harfbuzz.yaml +++ b/ansible/roles/compiled/tasks/common/harfbuzz.yaml @@ -13,7 +13,7 @@ - never - harfbuzz{{ item.version_number }} environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" block: - name: Download harfbuzz {{ version_number }} ansible.builtin.get_url: diff --git a/ansible/roles/compiled/tasks/common/hwloc.yaml b/ansible/roles/compiled/tasks/common/hwloc.yaml index a3800f68..bdcc66df 100644 --- a/ansible/roles/compiled/tasks/common/hwloc.yaml +++ b/ansible/roles/compiled/tasks/common/hwloc.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install hwloc {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/jemalloc.yaml b/ansible/roles/compiled/tasks/common/jemalloc.yaml index fdd0628e..7cf7271e 100644 --- a/ansible/roles/compiled/tasks/common/jemalloc.yaml +++ b/ansible/roles/compiled/tasks/common/jemalloc.yaml @@ -38,7 +38,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install jemalloc {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/lapack.yaml b/ansible/roles/compiled/tasks/common/lapack.yaml index 34f3b27a..23dcb640 100644 --- a/ansible/roles/compiled/tasks/common/lapack.yaml +++ b/ansible/roles/compiled/tasks/common/lapack.yaml @@ -43,7 +43,7 @@ chdir: "{{ build_dir }}" target: "all" environment: - MAKEFLAGS: "-j {{ ansible_processor_count }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_count'] }}" - name: Install LAPACK {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/mono.yaml b/ansible/roles/compiled/tasks/common/mono.yaml index 35f5cf6a..e69729cd 100644 --- a/ansible/roles/compiled/tasks/common/mono.yaml +++ b/ansible/roles/compiled/tasks/common/mono.yaml @@ -40,7 +40,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install mono {{ version_number }} community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/common/mpich.yaml b/ansible/roles/compiled/tasks/common/mpich.yaml index 05003fa4..a04db493 100644 --- a/ansible/roles/compiled/tasks/common/mpich.yaml +++ b/ansible/roles/compiled/tasks/common/mpich.yaml @@ -44,7 +44,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install mpich {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/openblas.yaml b/ansible/roles/compiled/tasks/common/openblas.yaml index c2324afe..376a16bd 100644 --- a/ansible/roles/compiled/tasks/common/openblas.yaml +++ b/ansible/roles/compiled/tasks/common/openblas.yaml @@ -33,7 +33,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_count }} {{ TARGET }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_count'] }} {{ TARGET }}" - name: Install OpenBLAS {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/openmpi.yaml b/ansible/roles/compiled/tasks/common/openmpi.yaml index ef8d7add..73f001ba 100644 --- a/ansible/roles/compiled/tasks/common/openmpi.yaml +++ b/ansible/roles/compiled/tasks/common/openmpi.yaml @@ -18,7 +18,7 @@ - never - openmpi{{ item.version_number }} environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" block: - name: Install OpenMPI {{ version_number }} block: diff --git a/ansible/roles/compiled/tasks/common/perl.yaml b/ansible/roles/compiled/tasks/common/perl.yaml index 81eb0b1c..5e9809bf 100644 --- a/ansible/roles/compiled/tasks/common/perl.yaml +++ b/ansible/roles/compiled/tasks/common/perl.yaml @@ -12,7 +12,7 @@ block: - name: Install perl using perlbrew {{ version_number }} - ansible.builtin.command: "/bin/bash -c 'module add perlbrew && perlbrew install -j {{ ansible_processor_vcpus }} perl-{{ version_number }}'" + ansible.builtin.command: "/bin/bash -c 'module add perlbrew && perlbrew install -j {{ ansible_facts['processor_vcpus'] }} perl-{{ version_number }}'" args: creates: "{{ install_dir }}" diff --git a/ansible/roles/compiled/tasks/common/pmix.yaml b/ansible/roles/compiled/tasks/common/pmix.yaml index 837cd0ac..f8155f42 100644 --- a/ansible/roles/compiled/tasks/common/pmix.yaml +++ b/ansible/roles/compiled/tasks/common/pmix.yaml @@ -43,7 +43,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install pmix {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/python.yaml b/ansible/roles/compiled/tasks/common/python.yaml index e844e003..8650f702 100644 --- a/ansible/roles/compiled/tasks/common/python.yaml +++ b/ansible/roles/compiled/tasks/common/python.yaml @@ -51,7 +51,7 @@ # params: # PROFILE_TASK="-m test.regrtest --pgo test_array test_base64 test_binascii test_binhex test_binop test_c_locale_coercion test_csv test_json test_hashlib test_unicode test_codecs test_traceback test_decimal test_math test_compile test_threading test_time test_fstring test_re test_float test_class test_cmath test_complex test_iter test_struct test_slice test_set test_dict test_long test_bytes test_memoryview test_io test_pickle" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install Python {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/ruby.yaml b/ansible/roles/compiled/tasks/common/ruby.yaml index 72a2ff09..9bb9f4a0 100644 --- a/ansible/roles/compiled/tasks/common/ruby.yaml +++ b/ansible/roles/compiled/tasks/common/ruby.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install ruby {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/singularity.yaml b/ansible/roles/compiled/tasks/common/singularity.yaml index 281a5448..4446907f 100644 --- a/ansible/roles/compiled/tasks/common/singularity.yaml +++ b/ansible/roles/compiled/tasks/common/singularity.yaml @@ -12,8 +12,8 @@ - never - singularity{{ item.version_number }} environment: - PATH: "{{ go_location }}:{{ ansible_env.PATH }}" - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + PATH: "{{ go_location }}:{{ ansible_facts['env'].PATH }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" block: - name: Install singularity {{ version_number }} when: "version_number.startswith('3') or version_number.startswith('4')" @@ -105,7 +105,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install singularity community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/common/slurm-drmaa.yaml b/ansible/roles/compiled/tasks/common/slurm-drmaa.yaml index 660613c4..6f948673 100644 --- a/ansible/roles/compiled/tasks/common/slurm-drmaa.yaml +++ b/ansible/roles/compiled/tasks/common/slurm-drmaa.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install DRMAA for Slurm {{ version_number }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/squashfuse.yaml b/ansible/roles/compiled/tasks/common/squashfuse.yaml index 07bccf4c..43d00f44 100644 --- a/ansible/roles/compiled/tasks/common/squashfuse.yaml +++ b/ansible/roles/compiled/tasks/common/squashfuse.yaml @@ -42,7 +42,7 @@ community.general.make: chdir: "{{ unzip_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install squashfuse community.general.make: chdir: "{{ unzip_dir }}" diff --git a/ansible/roles/compiled/tasks/common/ucx.yaml b/ansible/roles/compiled/tasks/common/ucx.yaml index 88885d12..76ce9be2 100644 --- a/ansible/roles/compiled/tasks/common/ucx.yaml +++ b/ansible/roles/compiled/tasks/common/ucx.yaml @@ -43,7 +43,7 @@ community.general.make: chdir: "{{ build_dir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install UCX {{ version_number }} to {{ install_dir }} community.general.make: chdir: "{{ build_dir }}" diff --git a/ansible/roles/compiled/tasks/common/zstd.yaml b/ansible/roles/compiled/tasks/common/zstd.yaml index 6eb20931..831ae1e3 100644 --- a/ansible/roles/compiled/tasks/common/zstd.yaml +++ b/ansible/roles/compiled/tasks/common/zstd.yaml @@ -28,7 +28,7 @@ community.general.make: chdir: "{{ unzipdir }}" environment: - MAKEFLAGS: "-j {{ ansible_processor_vcpus }}" + MAKEFLAGS: "-j {{ ansible_facts['processor_vcpus'] }}" - name: Install zstd {{ version_number }} community.general.make: chdir: "{{ unzipdir }}" diff --git a/ansible/roles/containers/templates/bio/bcbio.def b/ansible/roles/containers/templates/bio/bcbio.def index f6868a98..b5531e01 100644 --- a/ansible/roles/containers/templates/bio/bcbio.def +++ b/ansible/roles/containers/templates/bio/bcbio.def @@ -30,7 +30,7 @@ From: {{ base_container_image }} wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py # Install bcbio base - python3 bcbio_nextgen_install.py --cores {{ ansible_processor_vcpus }} --tooldir=/opt/bcbio_nextgen_tools --nodata --isolate /opt/bcbio_nextgen + python3 bcbio_nextgen_install.py --cores {{ ansible_facts['processor_vcpus'] }} --tooldir=/opt/bcbio_nextgen_tools --nodata --isolate /opt/bcbio_nextgen . /opt/bcbio_nextgen/anaconda/bin/activate bcbio_nextgen.py upgrade -u stable --genomes hg38 --aligners bwa --tools diff --git a/ansible/roles/containers/templates/common/RStudio.def b/ansible/roles/containers/templates/common/RStudio.def index 2e501bff..7822154e 100644 --- a/ansible/roles/containers/templates/common/RStudio.def +++ b/ansible/roles/containers/templates/common/RStudio.def @@ -160,7 +160,7 @@ From: {{ base_container_image }} "shiny", "tidyverse", "xtable" - ), Ncpus={{ ansible_processor_vcpus }})' + ), Ncpus={{ ansible_facts['processor_vcpus'] }})' Rscript -e 'update.packages(ask=FALSE)' Rscript -e 'devtools::install_github("hadley/devtools")' @@ -168,12 +168,12 @@ From: {{ base_container_image }} chmod ugo+w /var/run/rstudio-server chmod +t /var/run/rstudio-server - Rscript -e 'install.packages("BiocManager", Ncpus={{ ansible_processor_vcpus }})' + Rscript -e 'install.packages("BiocManager", Ncpus={{ ansible_facts['processor_vcpus'] }})' Rscript -e 'BiocManager::install(ask=FALSE, update=TRUE)' Rscript -e 'BiocManager::install( pkgs = c("DESeq2", "edgeR", "limma", "MethylSeekR", "methylKit", "bsseq"), - dependencies = TRUE, Ncpus={{ ansible_processor_vcpus }} + dependencies = TRUE, Ncpus={{ ansible_facts['processor_vcpus'] }} )' Rscript -e 'install.packages( @@ -182,7 +182,7 @@ From: {{ base_container_image }} "https://r.acidgenomics.com", BiocManager::repositories() ), - dependencies = TRUE, Ncpus={{ ansible_processor_vcpus }} + dependencies = TRUE, Ncpus={{ ansible_facts['processor_vcpus'] }} )' Rscript -e 'install.packages( @@ -191,7 +191,7 @@ From: {{ base_container_image }} "https://r.acidgenomics.com", BiocManager::repositories() ), - dependencies = TRUE, Ncpus={{ ansible_processor_vcpus }} + dependencies = TRUE, Ncpus={{ ansible_facts['processor_vcpus'] }} )' # Cleanup the container diff --git a/uv.lock b/uv.lock index 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