diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/pasta/package.py | 45 |
1 files changed, 29 insertions, 16 deletions
diff --git a/var/spack/repos/builtin/packages/pasta/package.py b/var/spack/repos/builtin/packages/pasta/package.py index 38ebc787e7..a69368c410 100644 --- a/var/spack/repos/builtin/packages/pasta/package.py +++ b/var/spack/repos/builtin/packages/pasta/package.py @@ -3,10 +3,12 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +from os import unlink + from spack.package import * -class Pasta(Package): +class Pasta(PythonPackage): """PASTA (Practical Alignment using SATe and Transitivity)""" homepage = "https://github.com/smirarab/pasta" @@ -16,10 +18,11 @@ class Pasta(Package): version("1.9.0", commit="370ae2d21ef461bcb2cef7c20cb5a4a1db7ff99d") version("1.8.3", commit="738bec5e0d5a18d013c193d7453374bed47456c9") - depends_on("python@3:", when="@1.9.0:") - depends_on("python@:2", when="@:1.8.3") - depends_on("py-dendropy") - depends_on("java") + depends_on("python@3:", when="@1.9.0:", type=("build", "run")) + depends_on("python@:2", when="@:1.8.3", type=("build", "run")) + depends_on("py-dendropy@4:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("java", type="run") resource( name="tools", @@ -31,14 +34,24 @@ class Pasta(Package): def setup_build_environment(self, env): tools = join_path(self.prefix, "sate-tools-linux") env.set("PASTA_TOOLS_DEVDIR", tools) - - def install(self, spec, prefix): - # build process for pasta is very hacky -- uses hard links to source - # install the tree first so links don't break - install_tree(".", prefix) - - # run the 'build' from within the prefix - python = which("python") - - with working_dir(prefix): - python("setup.py", "develop") + env.set("PASTA_TOOLS_RUNDIR", self.prefix.bin) + + def setup_run_environment(self, env): + env.set("PASTA_TOOLS_RUNDIR", self.prefix.bin) + + @run_before("install") + def install_resource(self): + with working_dir(self.stage.source_path): + tools = tools = join_path(self.prefix, "sate-tools-linux") + install_tree("sate-tools-linux", tools) + + @run_after("install") + def install_stragglers(self): + # install script negelects to actually copy some things + scripts = join_path(self.stage.source_path, "resources", "scripts") + with working_dir(scripts): + unlink(join_path(self.prefix.bin, "hmmeralign")) + install("hmmeralign", self.prefix.bin) + src_bin = join_path(self.stage.source_path, "bin") + with working_dir(src_bin): + install("treeshrink", self.prefix.bin) |