Conda installation requested and failed in local galaxy

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1

HI,

When I try to run galaxy local, I get the message “conda installation requested and failed”.
Error: did not recognise option ‘Book/Galaxy/galaxy/database/dependencies/_conda’, please try -h

I have gone into the galaxy.yml file and amended it as so:

conda_prefix: <tool_dependency_dir>/_conda

tool_dependency_dir: dependencies

conda_auto_init: true

I cannot understand what the issue is. Despite this, it allows me to open galaxy on the web and download tools but the tools do not work.

any help would be much appreciated!!

1 Like
2

These are the default setting, you don’t need to change them.
If you do, you need to replace <tool_dependency_dir>/ with a path, like conda_prefix: /Book/Galaxy/galaxy/database/dependencies/_conda/ , but again that isn’t necessary.

Can you be more specific about what you do to see these error messages. Are they in the user interface, or in the logs ?

I would also suggest reading https://docs.galaxyproject.org/en/master/admin/conda_faq.html if you haven’t, that might clear things up for you.

1 Like
3

@mvdbeek I run galaxy in the terminal

Then it says installing Conda, then it says Conda installation requested and failed (in the terminal). This happened before I even configured the galaxy.yml file. After failing to install, it repeats the process of trying to install Conda and fails again

I have read that page you suggested and from that made the changes to the galaxy.yml file. I am new to this, so have very little experience and I am struggling to understand some of the material.

1 Like
4

Hi @Lauren

The advice from @mvdbeek is very good. Unless an advanced admin configuration is needed for some reason, using all defaults can be a simple method to get a single-user local Galaxy instance running.

These instructions in prior Q&A explain the first steps when setting up a local under OSX. You might choose to start over, following the help, to see if that works for you. Example step-by-step for a basic local Galaxy install with an admin account created

The most current version of Galaxy is always listed here: https://docs.galaxyproject.org/en/master/releases/index.html

For even more administrative help, including tutorials and training resources, please see: Local Galaxy: Basic Question -- Installing more tools

5

thank you @jennaj

But I am still having issues and am unable to use local galaxy.

I have deleted and reinstalled it many times. I have followed the instructions from get galaxy and left everything as the default settings but when I run galaxy in the terminal using sh run.sh, it activates the virtual environment and then it gets to the point where galaxy wants to install conda but fails to do so, this cycle continues. Why might it be failing?

Activating virtualenv at .venv

galaxy.tool_util.deps WARNING 2020-03-31 12:11:48,004 Path ‘database/dependencies’ does not exist, ignoring

galaxy.tool_util.deps WARNING 2020-03-31 12:11:48,005 Path ‘database/dependencies’ is not directory, ignoring

galaxy.tool_util.deps.conda_util INFO 2020-03-31 12:11:48,183 Installing conda, this may take several minutes.

ERROR: did not recognize option ‘Book/Galaxy/galaxy/database/dependencies/_conda’, please try -h

galaxy.tool_util.deps.installable WARNING 2020-03-31 12:14:40,066 Conda installation requested and failed.

galaxy.tool_util.deps.conda_util INFO 2020-03-31 12:14:40,067 Installing conda, this may take several minutes.

I still get these error messages also:

galaxy.tools.toolbox.base ERROR 2020-03-31 12:17:57,604 [p:2741,w:0,m:0] [MainThread] Error reading tool configuration file from path ‘evolution/codingSnps.xml’: [Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/codingSnps.loc’

galaxy.tools.toolbox.base ERROR 2020-03-31 12:17:57,606 [p:2741,w:0,m:0] [MainThread] Error reading tool configuration file from path ‘evolution/add_scores.xml’: [Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/add_scores.loc’

galaxy.tools.toolbox.base ERROR 2020-03-31 12:17:57,645 [p:2741,w:0,m:0] [MainThread] Error reading tool configuration file from path ‘phenotype_association/sift.xml’: [Errno 2] No such file or directory: ‘/Volumes/My Book/Galaxy/galaxy/tool-data/sift_db.loc’

…Eventually it seems to give up after many DEBUG lines and I am provide with the http address but this takes a while to load in the web browser and the tools do not work.

I have python 3.7.7 installed on my Mac, this has now been set as the default and I have also recently updated my MacOS to Catalina.

Its getting very frustrating!

6

As far as I know you should not get this error: database/dependencies’ does not exist, ignoring if you really start over from the beginning and not change anything. If you re-install but use the same config.yml you are still doing the same.

Maybe it helps if you post the exact lines here again from galaxy/config/galaxy.yml that has to do with conda.

Also, try to do it step by step. With the information that you are giving now it is hard to help you.
So first download a fresh install, don’t change the config and start galaxy. Does this work? Can you start galaxy without errors and can you open the webinterface?

Second, change only the following lines to:
conda_auto_install: true
conda_auto_init: true

Try to start galaxy again, does it still work?

As last, I think this has not to do with you problem but check if there are no old hidden .conda folders. You can check it with the ls -la command. In your case a good thing to check is ls -la Book/Galaxy/

You could also install conda outside galaxy and tell galaxy where to find conda. But this can cause some permission/rights issues. Those issues are not hard to solve but you need some “commandline” experience.

7

Thank you @gbbio

I have completely reset my Mac (now using Catalina OS), installed Xcode, home-brew and python3 and then used the terminal to clone galaxy onto my external hard drive and I ran galaxy using sh run.sh but I still get the same outputs.

Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python3.7/site-packages (20.0.2)
Ignoring bz2file: markers ‘python_version < “3.3”’ don’t match your environment
Ignoring configparser: markers ‘python_version < “3.2”’ don’t match your environment
Ignoring contextlib2: markers ‘python_version < “3.5”’ don’t match your environment
Ignoring enum34: markers ‘python_version < “3.4”’ don’t match your environment
Ignoring funcsigs: markers ‘python_version < “3.3”’ don’t match your environment
Ignoring functools32: markers ‘python_version < “3.2”’ don’t match your environment
Ignoring futures: markers ‘python_version == “2.6” or python_version == “2.7”’ don’t match your environment
Ignoring ipaddress: markers ‘python_version < “3.3”’ don’t match your environment
Ignoring pathlib2: markers ‘python_version < “3.6”’ don’t match your environment
Ignoring pyinotify: markers ‘sys_platform != “win32” and sys_platform != “darwin” and sys_platform != “sunos5”’ don’t match your environment
Ignoring python-openid: markers ‘python_version < “3.0”’ don’t match your environment
Ignoring ruamel.ordereddict: markers ‘platform_python_implementation == “CPython” and python_version <= “2.7”’ don’t match your environment
Ignoring scandir: markers ‘python_version < “3.5”’ don’t match your environment
Ignoring subprocess32: markers ‘python_version < “3.0”’ don’t match your environment
Ignoring typing: markers ‘python_version < “3.5”’ don’t match your environment
Ignoring unicodecsv: markers ‘python_version < “3.0”’ don’t match your environment
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple

The Galaxy client has not yet been built and will be built now.
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warning hyphy-vision > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
warning hyphy-vision > alignment.js > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
warning hyphy-vision > alignment.js > phylotree > rollup-plugin-node-resolve@3.4.0: This package has been deprecated and is no longer maintained. Please use @rollup/plugin-node-resolve.
warning hyphy-vision > create-react-class > fbjs > core-js@1.2.7: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
warning hyphy-vision > alignment.js > @gmod/bam > @babel/runtime-corejs2 > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
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warning webpack > watchpack > chokidar > fsevents > node-pre-gyp > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
warning webpack > watchpack > chokidar > fsevents > node-pre-gyp > tar > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
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success Saved lockfile.
Building /Volumes/My Book/Galaxy/galaxy/config/plugins/visualizations/hyphyvision/
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Hash: cfc7880b36d01b3069ce
Version: webpack 4.42.1
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WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
This can impact web performance.
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WARNING in webpack performance recommendations:
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For more info visit https://webpack.js.org/guides/code-splitting/
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warning parcel-bundler > core-js@2.6.11: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
warning parcel-bundler > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
warning parcel-bundler > @parcel/fs > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
warning parcel-bundler > htmlnano > svgo > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
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warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning parcel-bundler > @parcel/watcher > chokidar > fsevents > node-pre-gyp > tar > mkdirp@0.5.4: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
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success Saved lockfile.
Building /Volumes/My Book/Galaxy/galaxy/config/plugins/visualizations/openlayers/
$ parcel build src/script.js -d static --no-source-maps
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[7] ./galaxy/scripts/utils/utils.js 10.4 KiB {2} {3} {4} {5} [built]
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| ./galaxy/scripts/toolshed/toolshed.groups.js 1.14 KiB [built]
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+ 1233 hidden modules

WARNING in moment
Multiple versions of moment found:
2.20.1 ./~/moment
2.22.2 ./~/pikaday/~/moment

WARNING in popper.js
Multiple versions of popper.js found:
1.14.7 ./~/popper.js
1.15.0 ./~/bootstrap-vue/~/popper.js

Check how you can resolve duplicate packages:

WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
This can impact web performance.
Assets:
assets/912ec66d7572ff821749319396470bde.svg (434 KiB)
base.css (523 KiB)
libs.chunk.js (1.97 MiB)
admin.bundled.js (1.35 MiB)
analysis.bundled.js (1.44 MiB)
generic.bundled.js (1020 KiB)
login.bundled.js (1.01 MiB)
vendors~ruleCollectionBuilder.chunk.js (1.03 MiB)

WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
Entrypoints:
login (3.49 MiB)
base.css
base.chunk.js
libs.chunk.js
login.bundled.js
analysis (3.92 MiB)
base.css
base.chunk.js
libs.chunk.js
analysis.bundled.js
admin (3.83 MiB)
base.css
base.chunk.js
libs.chunk.js
admin.bundled.js
generic (3.47 MiB)
base.css
base.chunk.js
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generic.bundled.js

/Volumes/My Book/Galaxy/galaxy
Activating virtualenv at .venv
galaxy.tool_util.deps WARNING 2020-04-01 14:42:04,343 Path ‘database/dependencies’ does not exist, ignoring
galaxy.tool_util.deps WARNING 2020-04-01 14:42:04,343 Path ‘database/dependencies’ is not directory, ignoring
galaxy.tool_util.deps.conda_util INFO 2020-04-01 14:42:04,480 Installing conda, this may take several minutes.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 44.0M 100 44.0M 0 0 258k 0 0:02:54 0:02:54 --:–:-- 282k
ERROR: did not recognize option ‘Book/Galaxy/galaxy/database/dependencies/_conda’, please try -h
galaxy.tool_util.deps.installable WARNING 2020-04-01 14:44:58,988 Conda installation requested and failed.
galaxy.tool_util.deps.conda_util INFO 2020-04-01 14:44:58,989 Installing conda, this may take several minutes.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 44.0M 100 44.0M 0 0 279k 0 0:02:41 0:02:41 --:–:-- 283k
ERROR: did not recognize option ‘Book/Galaxy/galaxy/database/dependencies/_conda’, please try -h
galaxy.tool_util.deps.installable WARNING 2020-04-01 14:47:40,314 Conda installation requested and failed.

I am eventually given a http link but I am assuming the tool still won’t work because the tools require Conda and Conda has not installed.

If I do this…
" only the following lines to:
conda_auto_install: true
conda_auto_init: true"

I still get:
Activating virtualenv at .venv
galaxy.tool_util.deps.conda_util INFO 2020-04-02 12:08:27,618 Installing conda, this may take several minutes.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 44.0M 100 44.0M 0 0 278k 0 0:02:41 0:02:41 --:–:-- 284k
ERROR: did not recognize option ‘Book/Galaxy/galaxy/database/dependencies/_conda’, please try -h
galaxy.tool_util.deps.installable WARNING 2020-04-02 12:11:09,670 Conda installation requested and failed.

How do I go about doing this….“You could also install conda outside galaxy and tell galaxy where to find conda. But this can cause some permission/rights issues. Those issues are not hard to solve but you need some “commandline” experience.”

would it be possible to install Conda where galaxy expects it to be i.e database/dependencies

thank you,

8

Ah! I think you have problems because of the space in your path.

Look at the error:
did not recognize option ‘Book/Galaxy/galaxy/database/dependencies/_conda
And look at the path that it should be:
/Volumes/My Book/Galaxy/galaxy/database/dependencies/_conda

Try to change /Volumes/My Book to something like /Volumes/My_Book. Besides your problem now you should not have spaces in folder or file names. Good luck and let us know if this solved it.

2 Likes
9

Hi @gbbio

I have edited my book to my_book, deleted and re-cloned galaxy and re-installed it and it has worked! Conda has installed.

Thank you!!

2 Likes