diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/augustus/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 32 |
1 files changed, 15 insertions, 17 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index e0e002d6fc..2c5cfa5c0d 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -69,7 +69,7 @@ class Augustus(MakefilePackage): filter_file("g++", spack_cxx, "makefile", string=True) filter_file( "g++ -I/usr/include/boost", - "{0} -I{1}".format(spack_cxx, self.spec["boost"].prefix.include), + f"{spack_cxx} -I{self.spec['boost'].prefix.include}", "src/subdir.mk", string=True, ) @@ -101,7 +101,7 @@ class Augustus(MakefilePackage): with working_dir(join_path("auxprogs", "filterBam", "src")): makefile = FileFilter("Makefile") - makefile.filter("BAMTOOLS = .*", "BAMTOOLS = {0}".format(bamtools)) + makefile.filter("BAMTOOLS = .*", f"BAMTOOLS = {bamtools}") makefile.filter("INCLUDES = *", "INCLUDES = -I$(BAMTOOLS)/include/bamtools ") if "bamtools@2.5:" in spec: makefile.filter( @@ -113,32 +113,30 @@ class Augustus(MakefilePackage): ) with working_dir(join_path("auxprogs", "bam2hints")): makefile = FileFilter("Makefile") - makefile.filter("/usr/include/bamtools", "{0}/include/bamtools".format(bamtools)) + makefile.filter("/usr/include/bamtools", f"{bamtools}/include/bamtools") if "bamtools@2.5:" in spec: makefile.filter( - "LIBS = -lbamtools -lz", - "LIBS = {0}/lib64" "/libbamtools.a -lz".format(bamtools), + "LIBS = -lbamtools -lz", f"LIBS = {bamtools}/lib64/libbamtools.a -lz" ) if "bamtools@:2.4" in spec: makefile.filter( - "LIBS = -lbamtools -lz", - "LIBS = {0}/lib/bamtools" "/libbamtools.a -lz".format(bamtools), + "LIBS = -lbamtools -lz", f"LIBS = {bamtools}/lib/bamtools/libbamtools.a -lz" ) if self.version < Version("3.4.0"): with working_dir(join_path("auxprogs", "bam2wig")): makefile = FileFilter("Makefile") # point tools to spack installations - makefile.filter("BCFTOOLS=.*$", "BCFTOOLS={0}/include".format(bcftools)) - makefile.filter("SAMTOOLS=.*$", "SAMTOOLS={0}/include".format(samtools)) - makefile.filter("HTSLIB=.*$", "HTSLIB={0}/include".format(htslib)) + makefile.filter("BCFTOOLS=.*$", f"BCFTOOLS={bcftools}/include") + makefile.filter("SAMTOOLS=.*$", f"SAMTOOLS={samtools}/include") + makefile.filter("HTSLIB=.*$", f"HTSLIB={htslib}/include") # fix bad linking dirs makefile.filter("$(SAMTOOLS)/libbam.a", "$(SAMTOOLS)/../lib/libbam.a", string=True) makefile.filter("$(HTSLIB)/libhts.a", "$(HTSLIB)/../lib/libhts.a", string=True) with working_dir(join_path("auxprogs", "checkTargetSortedness")): makefile = FileFilter("Makefile") - makefile.filter("SAMTOOLS.*=.*$", "SAMTOOLS={0}/include".format(samtools)) + makefile.filter("SAMTOOLS.*=.*$", f"SAMTOOLS={samtools}/include") makefile.filter("LIBS=-lbam", "LIBS=$(SAMTOOLS)/../lib/libbam.a", string=True) else: mysql = self.spec["mysql-client"].prefix @@ -147,12 +145,12 @@ class Augustus(MakefilePackage): with working_dir("src"): makefile = FileFilter("Makefile") - makefile.filter(r"/usr/include/mysql\+\+", "{0}/include/mysql++".format(mysqlpp)) + makefile.filter(r"/usr/include/mysql\+\+", f"{mysqlpp}/include/mysql++") if "^mariadb-c-client" in spec: - makefile.filter("/usr/include/mysql", "{0}/include/mariadb".format(mysql)) + makefile.filter("/usr/include/mysql", f"{mysql}/include/mariadb") else: - makefile.filter("/usr/include/mysql", "{0}/include/mysql".format(mysql)) - makefile.filter("/usr/include/lpsolve", "{0}/include/lpsolve".format(lpsolve)) + makefile.filter("/usr/include/mysql", f"{mysql}/include/mysql") + makefile.filter("/usr/include/lpsolve", f"{lpsolve}/include/lpsolve") def install(self, spec, prefix): install_tree("bin", join_path(self.spec.prefix, "bin")) @@ -163,12 +161,12 @@ class Augustus(MakefilePackage): def filter_sbang(self): with working_dir(self.prefix.scripts): pattern = "^#!.*" - repl = "#!{0}".format(self.spec["perl"].command.path) + repl = f"#!{self.spec['perl'].command.path}" files = glob.glob("*.pl") for file in files: filter_file(pattern, repl, *files, backup=False) - repl = "#!{0}".format(self.spec["python"].command.path) + repl = f"#!{self.spec['python'].command.path}" files = glob.glob("*.py") for file in files: filter_file(pattern, repl, *files, backup=False) |