Adding a lot of packages

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:

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

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]