HUMAnN update

[bebatut]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

---

This PR:

• Updates HUMAnN to the new version
• Updates the data manager for the reference databases and add utility mapping
• Creates new tests for HUMAnN (particularly of the database)
• Removes wrappers of utility scripts that are not available anymore, adds new ones but alos removes .xml to broken tools in current conda package (open PR on upstream tool)

@bernt-matthias I would love to have your feedback on this PR (if you have the time)

I renamed the folder from humann2 to hummann, similarly to what the tool developers did (now on GitHub).
It may help with further version updates, but it may break the current lineage.
Let me know if I should change that.

[bebatut]

I forgot that the PR of the conda package is still not merged: bioconda/bioconda-recipes#28066

[bernt-matthias]

Looks pretty good. Left a few comments. Not sure about tsv vs. tabular .. I think tabular is preferred.

Is tools/humann/generate_test_data still used to generate the test data? Would be great. Otherwise it should be removed.

[bebatut]

Not sure about tsv vs. tabular .. I think tabular is preferred.

I was not sure neither. I will change all to Tabular

[bebatut]

Is tools/humann/generate_test_data still used to generate the test data? Would be great. Otherwise it should be removed.

I remove it

[bebatut]

I do not understand why the last test for the DM is failing. It seems that the file or directory in which data need to be moved is not found but why?

Traceback (most recent call last):
  File "/home/bebatut/miniconda3/envs/planemo/lib/python3.8/shutil.py", line 791, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpvjz_sa5w/job_working_directory/000/3/working/dataset_1ab77dd5-9686-4664-bb8c-559708829db0_files/utility_mapping/full/map_uniref50_uniref90.txt.gz' -> '/tmp/tmpuaybbfbf/tmpzl1qn0cl/tmp3mb79mop/database/data_manager_tool-dataj82fe47_/humann/data/utility_mapping/utility_mapping-full-map_uniref50_uniref90-3.0.0-10052021'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpvjz_sa5w/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1733, in finish
    self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
  File "/tmp/tmpvjz_sa5w/galaxy-dev/lib/galaxy/tools/__init__.py", line 2707, in exec_after_process
    data_manager.process_result(out_data)
  File "/tmp/tmpvjz_sa5w/galaxy-dev/lib/galaxy/tools/data_manager/manager.py", line 301, in process_result
    self.process_move(data_table_name, name, output_ref_values[name].extra_files_path, **data_table_value)
  File "/tmp/tmpvjz_sa5w/galaxy-dev/lib/galaxy/tools/data_manager/manager.py", line 370, in process_move
    util.move_merge(source, target)
  File "/tmp/tmpvjz_sa5w/galaxy-dev/lib/galaxy/util/__init__.py", line 1476, in move_merge
    return shutil.move(source, target)
  File "/home/bebatut/miniconda3/envs/planemo/lib/python3.8/shutil.py", line 805, in move
    copy_function(src, real_dst)
  File "/home/bebatut/miniconda3/envs/planemo/lib/python3.8/shutil.py", line 435, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/home/bebatut/miniconda3/envs/planemo/lib/python3.8/shutil.py", line 264, in copyfile
    with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpuaybbfbf/tmpzl1qn0cl/tmp3mb79mop/database/data_manager_tool-dataj82fe47_/humann/data/utility_mapping/utility_mapping-full-map_uniref50_uniref90-3.0.0-10052021'

[bebatut]

Thanks a lot @bernt-matthias