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")