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augustus: add version 3.5.0 (#37037)

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Adjust dependencies and constraints.
This commit is contained in:
Glenn Johnson 2023-04-21 05:01:00 -05:00 committed by GitHub
parent 3303dcbfbd
commit b686974160
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1 changed files with 11 additions and 4 deletions
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15
var/spack/repos/builtin/packages/augustus/package.py
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@ -17,6 +17,7 @@ class Augustus(MakefilePackage):
url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz" url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
# Releases have moved to github # Releases have moved to github
version("3.5.0", sha256="5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686")
version("3.4.0", sha256="2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8") version("3.4.0", sha256="2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8")
version("3.3.2", sha256="d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2") version("3.3.2", sha256="d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2")
version( version(
@ -58,12 +59,12 @@ class Augustus(MakefilePackage):
# Trying to use filter_file here got too complicated so use a patch with a # Trying to use filter_file here got too complicated so use a patch with a
# corresponding environment variable # corresponding environment variable
patch("bam2wig_Makefile.patch", when="@3.4.0:") patch("bam2wig_Makefile.patch", when="@3.4.0")
def edit(self, spec, prefix): def edit(self, spec, prefix):
# Set compile commands for each compiler and # Set compile commands for each compiler and
# Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1) # 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")): with working_dir(join_path("auxprogs", "utrrnaseq", "Debug")):
filter_file("g++", spack_cxx, "makefile", string=True) filter_file("g++", spack_cxx, "makefile", string=True)
filter_file( filter_file(
@ -173,10 +174,16 @@ def filter_sbang(self):
filter_file(pattern, repl, *files, backup=False) filter_file(pattern, repl, *files, backup=False)
def setup_build_environment(self, env): 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) 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): def setup_run_environment(self, env):
env.set("AUGUSTUS_CONFIG_PATH", join_path(self.prefix, "config")) env.set("AUGUSTUS_CONFIG_PATH", join_path(self.prefix, "config"))
env.prepend_path("PATH", join_path(self.prefix, "scripts")) env.prepend_path("PATH", join_path(self.prefix, "scripts"))