How to install the sortmerna databases using the data manager?

[hepcat72]

I haven't done this before, so I apologize if this is a dumb question, but I tried running the data manager for sortmerna, but I get an error about missing .loc files in the galaxy log. Are there instructions I can consult on how to do the installation? I actually was able to run the data manager in my user account successfully. I just don't know how to get it to run in galaxy successfully.

The error in the log:

172.20.204.109 - [email protected] [18/Aug/2021:11:31:54 -0400] "GET /api/histories/7f1e6b427e67e752/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2021-08-18T15%3A31%3A50.000Z&qv=False&qv=False HTTP/1.1" 200 - "https://galaxy.princeton.edu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fdata_manager_sortmerna_database_downloader%2Fdata_manager_sortmerna_download%2F2.1b.1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/14.0.3 Safari/605.1.15"
Traceback (most recent call last):
  File "lib/galaxy/jobs/runners/__init__.py", line 540, in _finish_or_resubmit_job
    job_wrapper.finish(tool_stdout, tool_stderr, exit_code, check_output_detected_state=check_output_detected_state, job_stdout=job_stdout, job_stderr=job_stderr)
  File "lib/galaxy/jobs/__init__.py", line 1700, in finish
    self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
  File "lib/galaxy/tools/__init__.py", line 2560, in exec_after_process
    data_manager.process_result(out_data)
  File "lib/galaxy/tools/data_manager/manager.py", line 305, in process_result
    data_table.add_entry(data_table_value, persist=True, entry_source=self)
  File "lib/galaxy/tools/data/__init__.py", line 278, in add_entry
    self._add_entry(entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd)
  File "lib/galaxy/tools/data/__init__.py", line 646, in _add_entry
    data_table_fh = open(filename, 'wb')
FileNotFoundError: [Errno 2] No such file or directory: '/galaxy/galaxy-app/tool-data/toolshed.g2.bx.psu.edu/repos/rnateam/data_manager_sortmerna_database_downloader/7d2252852f96/rRNA_databases.loc'
galaxy.tools.error_reports DEBUG 2021-08-18 11:31:54,643 [p:32230,w:0,m:1] [SlurmRunner.work_thread-7] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f0d15db1438> generated response None
galaxy.util DEBUG 2021-08-18 11:31:54,668 [p:32230,w:0,m:1] [SlurmRunner.work_thread-7] Initiated SSL/TLS connection to SMTP server: smtp.princeton.edu

I ran the job from the galaxy interface:

I tried it a couple times.

When I run it on the command line, I don't seem to have an issue:

(base) bash-4.2$ python '/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/rnateam/data_manager_sortmerna_database_downloader/7d2252852f96/data_manager_sortmerna_database_downloader/data_manager/data_manager_sortmerna_download.py' --version 2.1b --jsonfile ./sortmerna_test.json
Starting...
Making ./sortmernatest
Download archive
Extract archive 2.1b.tar.gz
Moving fasta file from tmp/sortmerna-2.1b and index them
Outputting JSON
{"data_tables": {"rRNA_databases": [{"value": "2.1b-rfam-5.8s-database-id98", "name": "rfam-5.8s-database-id98", "path": "./sortmernatest/rRNA_databases/rfam-5.8s-database-id98"}, {"value": "2.1b-rfam-5s-database-id98", "name": "rfam-5s-database-id98", "path": "./sortmernatest/rRNA_databases/rfam-5s-database-id98"}, {"value": "2.1b-silva-arc-16s-id95", "name": "silva-arc-16s-id95", "path": "./sortmernatest/rRNA_databases/silva-arc-16s-id95"}, {"value": "2.1b-silva-arc-23s-id98", "name": "silva-arc-23s-id98", "path": "./sortmernatest/rRNA_databases/silva-arc-23s-id98"}, {"value": "2.1b-silva-bac-16s-id90", "name": "silva-bac-16s-id90", "path": "./sortmernatest/rRNA_databases/silva-bac-16s-id90"}, {"value": "2.1b-silva-bac-23s-id98", "name": "silva-bac-23s-id98", "path": "./sortmernatest/rRNA_databases/silva-bac-23s-id98"}, {"value": "2.1b-silva-euk-18s-id95", "name": "silva-euk-18s-id95", "path": "./sortmernatest/rRNA_databases/silva-euk-18s-id95"}, {"value": "2.1b-silva-euk-28s-id98", "name": "silva-euk-28s-id98", "path": "./sortmernatest/rRNA_databases/silva-euk-28s-id98"}]}}
Done.
(base) bash-4.2$ echo $?
0
(base) bash-4.2$ ls sortmernatest
rRNA_databases
(base) bash-4.2$ ls sortmernatest/rRNA_databases/
rfam-5.8s-database-id98  rfam-5s-database-id98	silva-arc-16s-id95  silva-arc-23s-id98	silva-bac-16s-id90  silva-bac-23s-id98	silva-euk-18s-id95  silva-euk-28s-id98
(base) bash-4.2$ ls -halF sortmernatest/rRNA_databases/
total 40K
drwxrwxr-x. 10 xxxxxx xxxxxx 4.0K Aug 18 12:11 ./
drwxrwxr-x.  3 xxxxxx xxxxxx 4.0K Aug 18 12:08 ../
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:08 rfam-5.8s-database-id98/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:08 rfam-5s-database-id98/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:09 silva-arc-16s-id95/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:09 silva-arc-23s-id98/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:10 silva-bac-16s-id90/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:10 silva-bac-23s-id98/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:11 silva-euk-18s-id95/
drwxrwxr-x.  2 xxxxxx xxxxxx 4.0K Aug 18 12:12 silva-euk-28s-id98/