def _fetch_bwa_indices(self):
genomes = []
for ref in os.listdir(self.reference):
# Downloads bowtie indexes genome(s)
genomes.append(ref)
#XXX: Should only accept bwa 0.5.x (binary bundled within deconseq), not 0.6.x indices
galaxy.rsync_genomes(self.reference, genomes, ["bwa"])
def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data")
self.progs = os.path.join(os.path.dirname(__file__), "data", "bin")
self.reference = os.path.join(os.path.dirname(__file__), "data", "reference")
self.bloom_dir = os.path.join(os.path.dirname(__file__), "data", "bloom")
self.custom_dir = os.path.join(os.path.dirname(__file__), "data", "custom")
self.synthetic_fastq = os.path.join(os.path.dirname(__file__), "data", "synthetic_fastq")
self.fastq_nreads = [1, 8, 200]
helpers._mkdir_p(self.data_dir)
helpers._mkdir_p(self.progs)
helpers._mkdir_p(self.reference)
helpers._mkdir_p(self.bloom_dir)
helpers._mkdir_p(self.custom_dir)
helpers._mkdir_p(self.synthetic_fastq)
# Check if 2bit decompressor is available
twobit_fa_path = os.path.join(self.progs, "twoBitToFa")
if not os.path.exists(twobit_fa_path):
galaxy.download_twoBitToFa_bin(twobit_fa_path)
# Downloads reference genome(s)
galaxy.rsync_genomes(self.reference, ["phix", "dm3", "ecoli"], ["ucsc"], twobit_fa_path)
# Collates results from all tests for later bulk reporting.
# This way runtime is not biased by connection delays.
self.results = []
def _fetch_bowtie_indices(self):
genomes = []
for ref in os.listdir(self.reference):
# Downloads bowtie indexes genome(s)
genomes.append(ref)
#XXX: parametrize for bowtie2, although it is possible that bowtie2 indices are
# not still properly generated in the Galaxy rsync :_(
galaxy.rsync_genomes(self.reference, genomes, ["bowtie"])
def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data")
self.progs = os.path.join(os.path.dirname(__file__), "data", "bin")
self.reference = os.path.join(os.path.dirname(__file__), "data", "reference")
self.bloom_dir = os.path.join(os.path.dirname(__file__), "data", "bloom")
self.custom_dir = os.path.join(os.path.dirname(__file__), "data", "custom")
self.synthetic_fastq = os.path.join(os.path.dirname(__file__), "data", "synthetic_fastq")
self.tmp = os.path.join(os.path.dirname(__file__), "data", "tmp")
helpers._mkdir_p(self.data_dir)
helpers._mkdir_p(self.progs)
helpers._mkdir_p(self.reference)
helpers._mkdir_p(self.bloom_dir)
helpers._mkdir_p(self.custom_dir)
helpers._mkdir_p(self.synthetic_fastq)
helpers._mkdir_p(self.tmp)
# SimNGS-specific variables
self.simngs_url = 'http://www.ebi.ac.uk/goldman-srv/simNGS/current/simNGS.tgz'
self.sim_reads = [100, 1000, 1000000, 10000000]
# simNGS will generate exactly the same "random" datasets on each run
self.sim_seed = "6666520666"
self.simngs = os.path.join(self.progs, "simNGS")
self.simlib = os.path.join(self.progs, "simLibrary")
# Default Illumina error profiles for simNGS
self.runfile = os.path.join(self.progs, "s_3_4x.runfile")
# Check if reference data is already downloaded, and do it if not
# Check if 2bit decompressor is available
twobit_fa_path = os.path.join(self.progs, "twoBitToFa")
if not os.path.exists(twobit_fa_path):
galaxy.download_twoBitToFa_bin(twobit_fa_path)
# Downloads reference genome(s)
galaxy.rsync_genomes(self.reference, ["phix", "dm3", "ecoli"], ["ucsc"], twobit_fa_path)
def setUp(self):
self.data_dir = os.path.join(os.path.dirname(__file__), "data")
self.progs = os.path.join(os.path.dirname(__file__), "data", "bin")
self.reference = os.path.join(os.path.dirname(__file__), "data", "reference")
self.bloom_dir = os.path.join(os.path.dirname(__file__), "data", "bloom")
self.custom_dir = os.path.join(os.path.dirname(__file__), "data", "custom")
self.synthetic_fastq = os.path.join(os.path.dirname(__file__), "data", "synthetic_fastq")
self.fastq_nreads = [1, 8, 200]
helpers._mkdir_p(self.data_dir)
helpers._mkdir_p(self.progs)
helpers._mkdir_p(self.reference)
helpers._mkdir_p(self.bloom_dir)
helpers._mkdir_p(self.custom_dir)
helpers._mkdir_p(self.synthetic_fastq)
# Check if 2bit decompressor is available
twobit_fa_path = os.path.join(self.progs, "twoBitToFa")
if not os.path.exists(twobit_fa_path):
galaxy.download_twoBitToFa_bin(twobit_fa_path)
# Downloads reference genome(s)
galaxy.rsync_genomes(self.reference, ["phix", "dm3", "ecoli"], ["ucsc"], twobit_fa_path)
def _fetch_bowtie_indices(self):
genomes = []
for ref in os.listdir(self.reference):
# Downloads (or builds) bowtie indexes genome(s)
genomes.append(ref)
galaxy.rsync_genomes(self.reference, genomes, ["bowtie", "bowtie2"])
