Some questions tool installation on my local Galaxy

Hi all,

I have installed about 30 tools on my local Galaxy 21.09 using shed-tools command (ephemeris). and have two issues. Has anyone ever had them?

  1. The second half of the tools described in the yaml file were not installed. In previous versions, some tools would fail as well, but I think the percentage was much smaller.

  2. The tool search form does not work. For example, I installed Anndata Operations as shown in first image, but typing anndata in the search form returns no results as shown second image.


I have been using 19.05 and have not had any problems. However, the shed-tool interface is no longer available, so I am testing 21.09. The above two issues seem to be the same for 21.05. My hosts are CentOS 7, 8 or Rocky Linux 8 virtual images(KVM) , 1 CPU and16 GB RAM.

Thank you,
Yukie

Additional info.
I found sometimes conda create takes long time even though it doesn’t take that long to execute conda directly on same host. Is this normal behavior?

Thank you,
Yukie

Hi, can you paste more infos? like the shed-tools error log? then, are you sure about the Galaxy server resources 1vpcu and 16GB of RAM is quite strange, Thanks.

Hi,

Thank you for your reply. Then I tested it on a server with 128GB RAM and it improved a lot.
Still, the conda process remains all the time. Output is following.

(64/66) Installing repository create_tool_recommendation_model from bgruening to section "Machine Learning" at revision afec8c595124 (TRT: 0:17:22.295197)
Timeout during install of create_tool_recommendation_model, extending wait to 1h
	repository create_tool_recommendation_model installed successfully (in 0:03:40.381343) at revision afec8c595124
(65/66) Installing repository crosscontamination_barcode_filter from iuc to section "RNA-seq" at revision 5ade5cf200da (TRT: 0:21:02.677362)
Timeout during install of crosscontamination_barcode_filter, extending wait to 1h
Traceback (most recent call last):
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
    chunked=chunked,
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
    six.raise_from(e, None)
  File "<string>", line 3, in raise_from
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
    httplib_response = conn.getresponse()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 1383, in getresponse
    response.begin()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 320, in begin
    version, status, reason = self._read_status()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 289, in _read_status
    raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
    raise six.reraise(type(error), error, _stacktrace)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 734, in reraise
    raise value.with_traceback(tb)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
    chunked=chunked,
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
    six.raise_from(e, None)
  File "<string>", line 3, in raise_from
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
    httplib_response = conn.getresponse()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 1383, in getresponse
    response.begin()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 320, in begin
    version, status, reason = self._read_status()
  File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 289, in _read_status
    raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 410, in install_repository_revision
    response = self.tool_shed_client.install_repository_revision(**repository)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxy/toolshed/__init__.py", line 144, in install_repository_revision
    return self._post(url=url, payload=payload)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxy/client.py", line 173, in _post
    files_attached=files_attached)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxyclient.py", line 123, in make_post_request
    timeout=self.timeout, allow_redirects=False)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/api.py", line 119, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/api.py", line 61, in request
    return session.request(method=method, url=url, **kwargs)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
    resp = self.send(prep, **send_kwargs)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
    r = adapter.send(request, **kwargs)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
    raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/yy/galaxy/.venv/bin/shed-tools", line 8, in <module>
    sys.exit(main())
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 629, in main
    **kwargs)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 176, in install_repositories
    result = self.install_repository_revision(repository, log)
  File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 448, in install_repository_revision
    start=start, msg=e.body,
AttributeError: 'ConnectionError' object has no attribute 'body'

The galaxy.log doesn’t seem to be giving any errors.

Thanks,
Yukie

conda create build the tool environment, the timing depends on the amount of dependencies of the tool

1 Like

if you run it again you receive the same error?

1 Like

Sorry for late,

Some of the tools worked, but others failed again. However, I think they cannot resolve dependency, because the installation does not finish forever when I run the conda create command directly as it appears in the logs.

Thanks,
Yukie