Question: install dependencies over conda
1
gravatar for marija.djurdjevic
4 months ago by
marija.djurdjevic30 wrote:

Hi, I have issue installing tool dependencies over conda (over Manage Tool Dependencies in Admin panel):

Traceback (most recent call last):
File "/home/data/galaxy_tool_dep/_conda/bin/conda", line 6, in <module>
  sys.exit(conda.cli.main())
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/cli/main.py", line 162, in main
  return conda_exception_handler(_main, *args)
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/exceptions.py", line 630, in conda_exception_handler
  return handle_exception(e)
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/exceptions.py", line 620, in handle_exception
  print_unexpected_error_message(e)
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/exceptions.py", line 578, in print_unexpected_error_message
  info_stdout, info_stderr = get_info()
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/exceptions.py", line 548, in get_info
  args.func(args, p)
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/cli/main_info.py", line 148, in execute
  from conda.api import get_index
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/api.py", line 1, in <module>
  from .core.index import get_index
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/core/index.py", line 8, in <module>
  from .package_cache import PackageCache
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/core/package_cache.py", line 10, in <module>
  from .path_actions import CacheUrlAction, ExtractPackageAction
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/core/path_actions.py", line 31, in <module>
  from ..gateways.download import download
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/conda/gateways/download.py", line 11, in <module>
  from requests.exceptions import ConnectionError, HTTPError, SSLError
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/requests/__init__.py", line 58, in <module>
  from . import utils
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/requests/utils.py", line 25, in <module>
  from . import certs
ImportError: cannot import name certs

If I run stand alone command:

/home/data/galaxy_tool_dep/_conda/bin/conda --debug create -y --name __hisat2@_uv_ hisat2

it works fine. What can be the issue?

Thanks,

Marija

ADD COMMENTlink modified 4 months ago • written 4 months ago by marija.djurdjevic30
1
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Make sure that Galaxy version 17_05 is used. Changes were made to help with Conda dependency resolution.

The most recently updated tools (including HISAT) should install all dependencies with Conda by default (even if Conda is available on the computer/server). Meaning, installing dependencies independently should not be needed.

I see your post at Github Conda: https://github.com/conda/conda/issues/5687. It will probably have replies stating that it is another version of the problem reported this prior post (and a few others): https://github.com/requests/requests/issues/2028. The help in that thread may be helpful in troubleshooting the problems with how conda is installed on your system.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson23k
0
gravatar for marija.djurdjevic
4 months ago by
marija.djurdjevic30 wrote:

Dear Jen,

Thanks for your response. I have the latest version of Galaxy and HISAT was just an example. I have the same issue installing other tool dependencies and even running tools which have conda dependencies.

I also went through a lot of posts everywhere, but unfortunately I couldn't solve my problem :(

Thanks once again, Marija

ADD COMMENTlink written 4 months ago by marija.djurdjevic30
2

Can you give us a outline what you have done? Essentially, you need to check that Conda is enabled in galaxy.ini, that during install you check a checkbox to install conda dependencies or enable conda_auto_install.

ADD REPLYlink written 4 months ago by Bjoern Gruening4.8k

Those are settings from galaxy.ini:

conda_prefix = /home/data/galaxy_tool_dep/_conda/
conda_exec = /home/data/galaxy_tool_dep/_conda/bin/conda
conda_debug = True
conda_ensure_channels = iuc,bioconda,r,defaults,conda-forge
conda_auto_install = True
conda_auto_init = True
conda_copy_dependencies = True

I install dependencies from Manage Tool Dependencies in Admin panel. I also tried to install tool dependencies from command line and it worked, but than I got the same error when I run the tool. I add some more info here: https://github.com/galaxyproject/galaxy/issues/4301

ADD REPLYlink written 4 months ago by marija.djurdjevic30
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