From 7018f02de8b15cf5b0ed70c11806e2e9f253894c Mon Sep 17 00:00:00 2001
From: Nicolas Richart <networms@gmail.ch>
Date: Fri, 21 Jun 2024 23:09:05 +0200
Subject: [PATCH] Adding a lot of packages
---
stacks/pinot-noir/modules.yaml | 29 ++++++++------
stacks/pinot-noir/packages_stack.yaml | 4 ++
stacks/pinot-noir/spack.yaml | 57 ++++++++++++++++++++++++++-
3 files changed, 77 insertions(+), 13 deletions(-)
diff --git a/stacks/pinot-noir/modules.yaml b/stacks/pinot-noir/modules.yaml
index 5d09950..99f6f3e 100644
--- a/stacks/pinot-noir/modules.yaml
+++ b/stacks/pinot-noir/modules.yaml
@@ -12,20 +12,25 @@ modules:
set:
${PACKAGE}_ROOT: ${PREFIX}
suffixes:
- +mpi: mpi
- +openmp: openmp
- threads=openmp: openmp
- ^fftw+openmp: openmp
- hdf5=parallel: h5
- +cuda: cuda
- +double-gpu: double-gpu
- +plumed: plumed
- +unwind: unwind
- +debug: dbg
- +ilp64: int64
- version_suffix=jl: julia
+ '+mpi': mpi
+ '+openmp': openmp
+ 'threads=openmp': openmp
+ '^fftw+openmp': openmp
+ 'hdf5=parallel': h5
+ '+cuda': cuda
+ '+double-gpu': double-gpu
+ '+plumed': plumed
+ '+unwind': unwind
+ '+debug': dbg
+ '+ilp64': int64
+ '+int64': int64
+ 'version_suffix=jl': julia
blacklist_implicits: true
+
+ blacklist:
+ - lmod
+
gcc:
environment:
set:
diff --git a/stacks/pinot-noir/packages_stack.yaml b/stacks/pinot-noir/packages_stack.yaml
index ebe093a..428a0e4 100644
--- a/stacks/pinot-noir/packages_stack.yaml
+++ b/stacks/pinot-noir/packages_stack.yaml
@@ -89,9 +89,13 @@ packages:
python:
require:
+ - spec: +ssl
- spec: +optimizations
when: '%gcc'
+ tk:
+ require: ['+xft', '+xss']
+
ucx:
require:
- spec: +rdmacm +rc +dc +ud +cma +verbs +vfs
diff --git a/stacks/pinot-noir/spack.yaml b/stacks/pinot-noir/spack.yaml
index 5cc9165..34f084b 100644
--- a/stacks/pinot-noir/spack.yaml
+++ b/stacks/pinot-noir/spack.yaml
@@ -25,18 +25,69 @@ spack:
# Core packages
# -------------------------------------------------------------------------
- core_codes:
+ - bzip2
+ - cmake
+ - emacs +tls
+ - fastqc
+ - fio
+ - git
+ - git-lfs
+ - gmp
- gnuplot
+ - gzip
- imagemagick +ghostscript
+ - intel-oneapi-advisor
+ - intel-oneapi-inspector
+ - intel-oneapi-vtune
+ - libarchive
+ - libjpeg-turbo
+ - libpng
+ - libtiff
+ - libxc
+ - libxml2
- lmod
+ - mpfr
+ - neovim
+ - parallel
+ - picard
+ - rclone
+ - sbt
+ - sratoolkit
+ - subversion
+ - tar
+ - tcl
+ - tk
+ - tmux
+ - trimmomatic
+ - valgrind
+ - xclip
+ - zlib
# -------------------------------------------------------------------------
# Serial codes
# -------------------------------------------------------------------------
- serial_codes:
- - python +ssl
+ - bwa
+ - fftw +openmp ~mpi
+ - fftw ~openmp ~mpi
+ - gsl
- hdf5 ~mpi
+ - hisat2
+ - htslib
+ - hwloc:
+ - intel-oneapi-tbb
+ - jasper
+ - mafft
- metis
+ - muscle
+ - nfft
+ - python
+ - scotch
+ - stacks
+ - star
+ - subread
- superlu
+ - voropp
# -------------------------------------------------------------------------
# Parallel codes
@@ -84,6 +135,10 @@ spack:
- [$core_codes]
- [$%system_compiler]
+ - matrix:
+ - [$cuda_system_codes]
+ - [$%system_compiler]
+
- matrix:
- [$serial_codes]
- [$%compilers]
--
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