I have run the following comands to create a conda env with the biobakery workflow.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install -c biobakery biobakery_workflows
conda install python=3.7
conda install -c biobakery leveldb
### run demo
biobakery_workflows_databases --install wmgx_demo
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/HD42R4_subsample.fastq.gz
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/HD32R1_subsample.fastq.gz
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/HD48R4_subsample.fastq.gz
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/LD96R2_subsample.fastq.gz
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/LV16R4_subsample.fastq.gz
wget https://github.com/biobakery/biobakery_workflows/raw/master/examples/tutorial/input/LV20R4_subsample.fastq.gz
mv *fastq.gz fastq/
## run demo
biobakery_workflows wmgx --input fastq/ --output demo_output/ --bypass-strain-profiling --local-jobs 6 --threads 2
On the last line of code (biobakery_workflows
), i get the following error:
Traceback (most recent call last):
File "/ home/emilyw/.conda/envs/biobakery/bin/wmgx.py", line 183, in <module>
workflow.go()
File "/home/emilyw/.conda/envs/biobakery/lib/python3.7/site-packages/anadama2/workflow.py", line 775, in go
task_idxs = nx.algorithms.dag.topological_sort(self.dag, reverse=True)
**TypeError: topological_sort() got an unexpected keyword argument 'reverse'**
Based on similar issues on other packages, it looks like the issue might be with some version inconsistency? Maybe a python/leveldb issue?