Correct Barcode tool error - networkx-related

[thi-trinh]

Hello,

I'm running a private instance of galaxy on AWS and have DuNovo 2.14 installed (same issue when using DuNovo 2.15). When running the correct barcodes tool on a valid "Make Families" output, it resulted in an error with the following log:

Fatal error: Exit code 1 () Info: ref_dir "refdir" not found. Creating.. families: /mnt/galaxy/files/000/dataset_338.dat refdir: refdir format: sam outfile: correct.sam outbase: correct.sam reads processed: 42270 reads with at least one reported alignment: 42168 (99.76%) reads that failed to align: 102 (0.24%) Reported 81752 alignments to 1 output stream(s) Success. Output located in "correct.sam". Traceback (most recent call last): File "/mnt/galaxy/tools/dunovo/2.14/nick/dunovo/fa563fa9b330/correct.py", line 12, in import networkx File "/mnt/galaxy/tools/networkx/1.10/iuc/package_networkx_1_10/e761775277c1/lib/python/networkx/init.py", line 68, in import networkx.utils File "/mnt/galaxy/tools/networkx/1.10/iuc/package_networkx_1_10/e761775277c1/lib/python/networkx/utils/init.py", line 2, in from networkx.utils.decorators import * File "/mnt/galaxy/tools/networkx/1.10/iuc/package_networkx_1_10/e761775277c1/lib/python/networkx/utils/decorators.py", line 7, in from decorator import decorator ImportError: No module named decorator

This tool works in the version 2.0.12 of du novo (which also requires networkx 1.10) but that package of du novo does not have some of the new tools I needed.

Any help on resolving this would be greatly appreciated.

Thanks

Thi

[thi-trinh]

This issue was resolved by disabling the installation of toolshed-managed repo/tools dependencies during the installation of DuNovo. The only dependencies left enabled are the ones managed by conda.

[NickSto]

Thanks for reporting, @thi-trinh. I'm re-opening this to track the issue when installing via toolshed, which is still supported in the code for now (probably deprecated in the future).