def _index_to_galaxy(work_dir, ref_file, gid, genome_indexes, config):
"""Index sequence files and update associated Galaxy loc files.
"""
indexes = {}
with cd(work_dir):
for idx in genome_indexes:
index_file = get_index_fn(idx)(ref_file)
if index_file:
indexes[idx] = os.path.join(work_dir, index_file)
galaxy.prep_locs(gid, indexes, config)
def _index_to_galaxy(work_dir, ref_file, gid, genome_indexes, config):
"""Index sequence files and update associated Galaxy loc files.
"""
indexes = {}
with cd(work_dir):
for idx in genome_indexes:
index_file = get_index_fn(idx)(ref_file)
if index_file:
indexes[idx] = os.path.join(work_dir, index_file)
galaxy.prep_locs(gid, indexes, config)
def _index_to_galaxy(work_dir, ref_file, gid, genome_indexes, config):
"""Index sequence files and update associated Galaxy loc files.
"""
INDEX_FNS = {
"seq" : _index_sam,
"bwa" : _index_bwa,
"bowtie": _index_bowtie,
"bowtie2": _index_bowtie2,
"maq": _index_maq,
"mosaik": _index_mosaik,
"novoalign": _index_novoalign,
"novoalign_cs": _index_novoalign_cs,
"ucsc": _index_twobit,
"eland": _index_eland,
"bfast": _index_bfast,
"arachne": _index_arachne
}
indexes = {}
with cd(work_dir):
for idx in genome_indexes:
index_file = INDEX_FNS[idx](ref_file)
if index_file:
indexes[idx] = os.path.join(work_dir, index_file)
galaxy.prep_locs(gid, indexes, config)
def _index_to_galaxy(work_dir, ref_file, gid, genome_indexes, config):
"""Index sequence files and update associated Galaxy loc files.
"""
INDEX_FNS = {
"seq": _index_sam,
"bwa": _index_bwa,
"bowtie": _index_bowtie,
"bowtie2": _index_bowtie2,
"maq": _index_maq,
"mosaik": _index_mosaik,
"novoalign": _index_novoalign,
"novoalign_cs": _index_novoalign_cs,
"ucsc": _index_twobit,
"eland": _index_eland,
"bfast": _index_bfast,
"arachne": _index_arachne
}
indexes = {}
with cd(work_dir):
for idx in genome_indexes:
index_file = INDEX_FNS[idx](ref_file)
if index_file:
indexes[idx] = os.path.join(work_dir, index_file)
galaxy.prep_locs(gid, indexes, config)