diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/isescan/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/isescan/package.py | 76 |
1 files changed, 39 insertions, 37 deletions
diff --git a/var/spack/repos/builtin/packages/isescan/package.py b/var/spack/repos/builtin/packages/isescan/package.py index 2896d87e00..c109f68ce1 100644 --- a/var/spack/repos/builtin/packages/isescan/package.py +++ b/var/spack/repos/builtin/packages/isescan/package.py @@ -8,64 +8,66 @@ from spack.package import * class Isescan(Package): """A python pipeline to identify IS (Insertion Sequence) elements in - genome and metagenome""" + genome and metagenome""" homepage = "https://github.com/xiezhq/ISEScan" - url = "https://github.com/xiezhq/ISEScan/archive/v1.7.2.1.tar.gz" + url = "https://github.com/xiezhq/ISEScan/archive/v1.7.2.1.tar.gz" - version('1.7.2.1', sha256='b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d') + version("1.7.2.1", sha256="b971a3e86a8cddaa4bcd520ba9e75425bbe93190466f81a3791ae0cb4baf5e5d") - depends_on('python@3.3.3:', type='run') - depends_on('py-numpy@1.8.0:', type='run') - depends_on('py-scipy@0.13.1:', type='run') - depends_on('py-biopython@1.62:', type='run') - depends_on('py-fastcluster', type='run') - depends_on('py-argparse', when='^python@:2.6,3.0:3.1', type='run') - depends_on('blast-plus@2.2.31:', type='run') - depends_on('fraggenescan@:1.30', type='run') - depends_on('hmmer@3.1b2:', type='run') + depends_on("python@3.3.3:", type="run") + depends_on("py-numpy@1.8.0:", type="run") + depends_on("py-scipy@0.13.1:", type="run") + depends_on("py-biopython@1.62:", type="run") + depends_on("py-fastcluster", type="run") + depends_on("py-argparse", when="^python@:2.6,3.0:3.1", type="run") + depends_on("blast-plus@2.2.31:", type="run") + depends_on("fraggenescan@:1.30", type="run") + depends_on("hmmer@3.1b2:", type="run") def setup_run_environment(self, env): - env.prepend_path('PATH', self.prefix) - env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'ssw201507')) + env.prepend_path("PATH", self.prefix) + env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "ssw201507")) def install(self, spec, prefix): # build bundled SSW library - with working_dir('ssw201507'): + with working_dir("ssw201507"): Executable(spack_cc)( - '-O3', '-pipe', self.compiler.cc_pic_flag, '-shared', - '-rdynamic', '-o', 'libssw.' + dso_suffix, 'ssw.c', 'ssw.h', + "-O3", + "-pipe", + self.compiler.cc_pic_flag, + "-shared", + "-rdynamic", + "-o", + "libssw." + dso_suffix, + "ssw.c", + "ssw.h", ) # set paths to required programs - blast_pfx = self.spec['blast-plus'].prefix.bin + blast_pfx = self.spec["blast-plus"].prefix.bin blastn_path = blast_pfx.blastn blastp_path = blast_pfx.blastp makeblastdb_path = blast_pfx.makeblastdb - hmmer_pfx = self.spec['hmmer'].prefix.bin + hmmer_pfx = self.spec["hmmer"].prefix.bin phmmer_path = hmmer_pfx.phmmer hmmsearch_path = hmmer_pfx.hmmsearch - fgs_pfx = self.spec['fraggenescan'].prefix.bin - fgs_path = join_path(fgs_pfx, 'run_FragGeneScan.pl') + fgs_pfx = self.spec["fraggenescan"].prefix.bin + fgs_path = join_path(fgs_pfx, "run_FragGeneScan.pl") - constants = FileFilter('constants.py') + constants = FileFilter("constants.py") - constants.filter('/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl', - fgs_path, string=True) - constants.filter('/apps/inst/hmmer-3.3/bin/phmmer', - phmmer_path, string=True) - constants.filter('/apps/inst/hmmer-3.3/bin/hmmsearch', - hmmsearch_path, string=True) - constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastn', - blastn_path, string=True) - constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/blastp', - blastp_path, string=True) - constants.filter('/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb', - makeblastdb_path, string=True) + constants.filter("/apps/inst/FragGeneScan1.30/run_FragGeneScan.pl", fgs_path, string=True) + constants.filter("/apps/inst/hmmer-3.3/bin/phmmer", phmmer_path, string=True) + constants.filter("/apps/inst/hmmer-3.3/bin/hmmsearch", hmmsearch_path, string=True) + constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastn", blastn_path, string=True) + constants.filter("/apps/inst/ncbi-blast-2.10.0+/bin/blastp", blastp_path, string=True) + constants.filter( + "/apps/inst/ncbi-blast-2.10.0+/bin/makeblastdb", makeblastdb_path, string=True + ) # install the whole tree - install_tree('.', prefix) - set_executable(join_path(prefix, 'isescan.py')) + install_tree(".", prefix) + set_executable(join_path(prefix, "isescan.py")) |