def test_restage(self):
stage = Stage(archive_url, name=stage_name)
stage.fetch()
stage.expand_archive()
stage.chdir_to_archive()
self.check_expand_archive(stage, stage_name)
self.check_chdir_to_archive(stage, stage_name)
# Try to make a file in the old archive dir
with closing(open('foobar', 'w')) as file:
file.write("this file is to be destroyed.")
self.assertTrue('foobar' in os.listdir(stage.expanded_archive_path))
# Make sure the file is not there after restage.
stage.restage()
self.check_chdir(stage, stage_name)
self.check_fetch(stage, stage_name)
stage.chdir_to_archive()
self.check_chdir_to_archive(stage, stage_name)
self.assertFalse('foobar' in os.listdir(stage.expanded_archive_path))
stage.destroy()
self.check_destroy(stage, stage_name)
def test_restage(self):
stage = Stage(archive_url, name=stage_name)
stage.fetch()
stage.expand_archive()
stage.chdir_to_archive()
self.check_expand_archive(stage, stage_name)
self.check_chdir_to_archive(stage, stage_name)
# Try to make a file in the old archive dir
with closing(open('foobar', 'w')) as file:
file.write("this file is to be destroyed.")
self.assertTrue('foobar' in os.listdir(stage.expanded_archive_path))
# Make sure the file is not there after restage.
stage.restage()
self.check_chdir(stage, stage_name)
self.check_fetch(stage, stage_name)
stage.chdir_to_archive()
self.check_chdir_to_archive(stage, stage_name)
self.assertFalse('foobar' in os.listdir(stage.expanded_archive_path))
stage.destroy()
self.check_destroy(stage, stage_name)
def test_expand_archive(self):
stage = Stage(archive_url, name=stage_name)
stage.fetch()
self.check_setup(stage, stage_name)
self.check_fetch(stage, stage_name)
stage.expand_archive()
self.check_expand_archive(stage, stage_name)
stage.destroy()
self.check_destroy(stage, stage_name)
def test_expand_archive(self):
stage = Stage(archive_url, name=stage_name)
stage.fetch()
self.check_setup(stage, stage_name)
self.check_fetch(stage, stage_name)
stage.expand_archive()
self.check_expand_archive(stage, stage_name)
stage.destroy()
self.check_destroy(stage, stage_name)
def install(self, spec, prefix):
build_dir = join_path(self.stage.source_path, "builddir")
os.mkdir(build_dir)
stage1 = Stage("https://github.com/ncbi/ngs/archive/1.1.3.tar.gz") # Download tarball. fetch() doesn't work with git url?
stage1.fetch()
stage1.expand_archive()
with working_dir(stage1.source_path):
ngs_build = join_path(stage1.source_path,"builddir")
os.mkdir(ngs_build)
configure("--build-prefix="+ ngs_build, "--prefix=" + prefix)
make("ngs-sdk")
make("ngs-python")
make("ngs-java")
configure("--build-prefix=" + ngs_build, "--with-ngs-sdk=" + prefix, "--prefix=" + prefix)
make("ngs-bam")
make("install")
stage2 = Stage("https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz")
stage2.fetch()
stage2.expand_archive()
with working_dir(stage2.source_path):
vdb_build = join_path(stage2.source_path,"builddir")
os.mkdir(vdb_build)
configure("--build-prefix=" + vdb_build,"--with-ngs-sdk-prefix=" + prefix, "--with-ngs-java-prefix=" + prefix, "--prefix=" + prefix)
make()
make("install")
# sra-tools build block
with working_dir(self.stage.source_path):
configure("--build-prefix=" + build_dir,
"--with-ngs-sdk-prefix=" + prefix, "--with-ncbi-vdb-build=" + vdb_build, "--with-ncbi-vdb-sources=" + stage2.source_path,
"--prefix=" + prefix)
make()
make("install")
