import os
import assnake
snake_module = assnake.SnakeModule(name='assnake-core-mapping',
install_dir=os.path.dirname(
os.path.abspath(__file__)))
import os, assnake
import assnake_anvio.result
from assnake.utils import read_yaml
this_dir = os.path.dirname(os.path.abspath(__file__))
snake_module = assnake.SnakeModule(name='assnake-anvio',
install_dir=this_dir,
results=[assnake_anvio.result],
snakefiles=[],
invocation_commands=[])
import os
import assnake
# from assnake_core_assembly.megahit.cmd_megahit import megahit_invocation
from assnake.utils.general import read_yaml
from assnake_core_binning.checkm.invocation_commands import chekcm_invocation
from assnake_core_binning.metabat2.invocation_commands import metabat2_invocation
this_dir = os.path.dirname(os.path.abspath(__file__))
snake_module = assnake.SnakeModule(
name='assnake-core-binning',
install_dir=this_dir,
snakefiles=['./metabat2/metabat2.smk', './checkm/checkm.smk'],
invocation_commands=[chekcm_invocation, metabat2_invocation],
wc_configs=[])
import os, assnake
snake_module = assnake.SnakeModule(
name='assnake-core-preprocessing',
install_dir=os.path.dirname(os.path.abspath(__file__)),
)
import os
import assnake
from assnake_core_taxonomy.metaphlan2.init_metaphlan2 import mp2_init
from assnake_core_taxonomy.metaphlan2.loaders import load_metaphlan2
snake_module = assnake.SnakeModule(
name='assnake-core-taxonomy',
install_dir=os.path.dirname(os.path.abspath(__file__)),
initialization_commands=[mp2_init],
dataset_methods={'load_metaphlan2': load_metaphlan2})
import os
import assnake
from assnake_dada2.invocation_commands import dada2_full
from assnake_dada2.init_dada2 import dada2_init
snake_module = assnake.SnakeModule(
name='assnake-dada2',
install_dir=os.path.dirname(os.path.abspath(__file__)),
snakefiles=[
'./assign_taxa/workflow.smk',
'./remove_chimeras/workflow.smk',
'./make_seqtab/workflow.smk',
'./derep_infer_merge/workflow.smk',
'./idtaxa/workflow.smk',
# './derep_infer_pooled/workflow.smk',
'./track_reads/workflow.smk',
],
invocation_commands=[dada2_full],
initialization_commands=[dada2_init])
import os
import assnake
snake_module = assnake.SnakeModule(
name='assnake-transcriptome',
install_dir=os.path.dirname(os.path.abspath(__file__)),
)
import os, assnake
import assnake_core_assembly.megahit.result as megahit
snake_module = assnake.SnakeModule(name='assnake-core-assembly',
install_dir=os.path.dirname(os.path.abspath(__file__)),
# results = [megahit]
)