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| author | Glenn Johnson <glenn-johnson@uiowa.edu> | 2023-04-21 05:01:00 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-04-21 12:01:00 +0200 |
| commit | b68697416017da46ca179f2d77b7edda0fb3b193 (patch) | |
| tree | c09ef84a30a8bda4edbac5e3e2052ea863762ed3 | |
| parent | 3303dcbfbdef50390e112308f8aedf5e2e4fe603 (diff) | |
| download | spack-b68697416017da46ca179f2d77b7edda0fb3b193.tar.gz spack-b68697416017da46ca179f2d77b7edda0fb3b193.tar.bz2 spack-b68697416017da46ca179f2d77b7edda0fb3b193.tar.xz spack-b68697416017da46ca179f2d77b7edda0fb3b193.zip | |
augustus: add version 3.5.0 (#37037)
Adjust dependencies and constraints.
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 15 |
1 files changed, 11 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index e10603e1e5..5aad912934 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -17,6 +17,7 @@ class Augustus(MakefilePackage): url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz" # Releases have moved to github + version("3.5.0", sha256="5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686") version("3.4.0", sha256="2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8") version("3.3.2", sha256="d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2") version( @@ -58,12 +59,12 @@ class Augustus(MakefilePackage): # Trying to use filter_file here got too complicated so use a patch with a # corresponding environment variable - patch("bam2wig_Makefile.patch", when="@3.4.0:") + patch("bam2wig_Makefile.patch", when="@3.4.0") def edit(self, spec, prefix): # Set compile commands for each compiler and # Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1) - if self.version >= Version("3.3.1-tag1"): + if "@3.3.1-tag1:3.4.0" in spec: with working_dir(join_path("auxprogs", "utrrnaseq", "Debug")): filter_file("g++", spack_cxx, "makefile", string=True) filter_file( @@ -173,10 +174,16 @@ class Augustus(MakefilePackage): filter_file(pattern, repl, *files, backup=False) def setup_build_environment(self, env): - if self.version >= Version("3.4.0"): - htslib = self.spec["htslib"].prefix + htslib = self.spec["htslib"].prefix + bamtools = self.spec["bamtools"].prefix + + if "@3.4.0" in self.spec: env.set("HTSLIBDIR", htslib) + if "@3.5.0:" in self.spec: + env.set("HTSLIB_INSTALL_DIR", htslib) + env.set("BAMTOOLS_INSTALL_DIR", bamtools) + def setup_run_environment(self, env): env.set("AUGUSTUS_CONFIG_PATH", join_path(self.prefix, "config")) env.prepend_path("PATH", join_path(self.prefix, "scripts")) |