For my own experiment, I want to execute 'run-job' from my local directory fasta and json files. I tried the same way mentioned here but it tries to download via url. How can I stop this download and use archive, metadata just from my local directory?
I created a new folder and created two new folders named 'data' and 'output'.
data
fastaFiles.zip
dataset (all the .fasta files are here)
fastaFiles-dataset.json
INFO started experiment 'subtype-k=4' (1/2)
INFO using random seed value 2996047997
INFO started step 'select' (1/3)
INFO started running pick_group
INFO retrieving 'https://raw.githubusercontent.com/stephensolis/kameris-experiments/master/files.yml'
ERROR an unexpected error occurred: KeyError: fastafiles-dataset
ERROR if you believe this is a bug, please report it at https://github.com/stephensolis/kameris/issues and include ALL the following text:
Traceback (most recent call last):
File "/home/shoumik/Thesis/kameris-1.2.3/kameris/main.py", line 41, in main
run_module.run(args)
File "/home/shoumik/Thesis/kameris-1.2.3/kameris/subcommands/run_job.py", line 276, in run
run_experiment_steps(steps, exp_options)
File "/home/shoumik/Thesis/kameris-1.2.3/kameris/subcommands/run_job.py", line 180, in run_experiment_steps
step_runners[step_options['type']](step_options, exp_options)
File "/home/shoumik/Thesis/kameris-1.2.3/kameris/job_steps/selection.py", line 60, in run_select_step
'metadata'
File "/home/shoumik/Thesis/kameris-1.2.3/kameris/utils/download_utils.py", line 61, in url_for_file
return urls[filetype][filename]
KeyError: u'fastafiles-dataset'
I created a new folder and created two new folders named 'data' and 'output'. data
fastaFiles-dataset.json
INFO started experiment 'subtype-k=4' (1/2) INFO using random seed value 2996047997 INFO started step 'select' (1/3) INFO started running pick_group INFO retrieving 'https://raw.githubusercontent.com/stephensolis/kameris-experiments/master/files.yml' ERROR an unexpected error occurred: KeyError: fastafiles-dataset ERROR if you believe this is a bug, please report it at https://github.com/stephensolis/kameris/issues and include ALL the following text: Traceback (most recent call last): File "/home/shoumik/Thesis/kameris-1.2.3/kameris/main.py", line 41, in main run_module.run(args) File "/home/shoumik/Thesis/kameris-1.2.3/kameris/subcommands/run_job.py", line 276, in run run_experiment_steps(steps, exp_options) File "/home/shoumik/Thesis/kameris-1.2.3/kameris/subcommands/run_job.py", line 180, in run_experiment_steps step_runners[step_options['type']](step_options, exp_options) File "/home/shoumik/Thesis/kameris-1.2.3/kameris/job_steps/selection.py", line 60, in run_select_step 'metadata' File "/home/shoumik/Thesis/kameris-1.2.3/kameris/utils/download_utils.py", line 61, in url_for_file return urls[filetype][filename] KeyError: u'fastafiles-dataset'