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databio / peppro

A modular, containerized pipeline for PRO-seq data processing
http://peppro.databio.org/
BSD 2-Clause "Simplified" License
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looper run errors #76

Closed Dale12138 closed 2 years ago

Dale12138 commented 4 years ago

Hi, I have encountered errors even in the very first step (dry run the example). I would appreciate it so much if you can drop me some hints on how to fix this! my code looper run peppro_test.yaml -d printouts Command: run (Looper version: 0.12.6) Reading sample annotations sheet: '/hpf/largeprojects/mdwilson/liangxi/projects/rela/chroseq/analysis/peppro/test/peppro_test.csv' Storing sample table from file '/hpf/largeprojects/mdwilson/liangxi/projects/rela/chroseq/analysis/peppro/test/peppro_test.csv' Traceback (most recent call last): File "/hpf/tools/centos6/python/2.7.9/bin/looper", line 10, in sys.exit(main()) File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/looper/looper.py", line 798, in main file_checks=args.file_checks, compute_env_file=getattr(args, 'env', None)) File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/looper/project.py", line 40, in init no_compute_exception=RuntimeError, **kwargs) File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/peppy/project.py", line 268, in init self._set_basic_samples() File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/peppy/project.py", line 1145, in _set_basic_samples self._samples = self._prep_samples() File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/peppy/project.py", line 1086, in _prep_samples sample = Sample(row.dropna(), prj=self) File "/hpf/tools/centos6/python/2.7.9/lib/python2.7/site-packages/peppy/sample.py", line 154, in init series = series.to_dict(OrderedDict) TypeError: to_dict() takes exactly 1 argument (2 given)

P.S I ve been using python/2.7.9

jpsmith5 commented 4 years ago

Hey @Dale12138, As the python people no longer are updating and supporting python2, so follows most of our tools. Can you give it an install with python3 and see how it goes? I’ll also make a note to update our documentation to emphasize this going forward.

Let us know if you hit a snag and we can definitely help troubleshoot.

Dale12138 commented 4 years ago

Oh, I didn't notice this python2 vs python3 discrepency here. I ll try to update the tools and dependencies to python3 and let you know! Thanks!

nsheff commented 2 years ago

@Dale12138 were you able to get this to work?

nsheff commented 2 years ago

Please reopen if you run into similar issues again.