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"])