toolshed not working anymore with old galaxy?

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Hi all,

since some months we are having an issue with the toolshed. It’s not installing any tools anymore printing the following error:
“Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable third-party cookies in your browser.”
I tried the enabling of third party cookies but it does not change anything.
Our instance is quite old (16.07) but a the moment we cannnot update.

Is there anything I can do to get access to the toolshed again?

I found a number of related topics, which are not helping with my problem:

Cheers
Jochen

2 Likes
2

Hi Jochen @bimbam23

I’ve asked your question on the developer’s gitter channel to see if there are any more potential solutions. They may answer here or there and you can certainly join in the chat: https://gitter.im/galaxyproject/dev?at=6014286f24cd6b60d8059a2c

My guess is that the upgrades that occurred this week are incompatible with the version of Galaxy you are using – or are incompatible right now – but let’s get more advice.

Good to see you (virtually) again!

3

Hej Jenn,

thanks for helping and good to hear from you too :slight_smile:

I will have a look at the gitter channel

Cheers Jochen

1 Like
4

Hi Jochen,

I have exactly the same problem - older Galaxy version (16.?) and cannot install any new tools. What did you find out and/or end up doing??

Best
Michael

5

Hi Michael,

I could not solve the problem. I might have to install a new galaxy version in the future… Updating from 16 …might be a bit difficult I guess.

Cheers
Jochen

6

Thanks for the information! Yes - I tried to update from version 16 (I think to 19) last year and could it kept failing.

We purchased Galaxy already installed on a Linux server from Bioteam - who maintained the updates until 2019 (i.e. Version 16). Unfortunately they stopped supporting us (and everyone else I gather) - but kindly left instructions on how to update it - which didn’t work. Since then we haven’t needed to update - until now when the Toolshed stopped working.

If you having any advice on updating - let me know.

Thanks
Michael

1 Like
7

For some details check out release 20.09 possibly broke the ability to install tools · Issue #11746 · galaxyproject/galaxy · GitHub

tldr: you have to update

2 Likes
8

To add, if you’re running into problems updating your Galaxy instances, let us know.
For such old releases I’d recommend doing year-by-year updates.

So if you start on release_16.01, I’d recommend updating to release_17.01, doing the database migrations (./manage_db.sh -c config/galaxy.ini), start up Galaxy and verify the interface works, and then going to release_18.01 and so on. Once you reach release_20.01 you have to migrate to Python 3, instructions for updating this are here: Supported Python versions — Galaxy Project 21.01 documentation

1 Like
9

Thanks for the tips. I did try to upgrade from 16 to 19 directly - but I guess I was too greedy. You guys do such a good job of putting out updates that it is hard to keep up.

In a similar vein - apart from Python 3 - do the newer Galaxy versions have higher Linux version requirements??

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Not that I am aware of, as long as you can install Python 3 somehow you should be good

11

Hi - I am running into problems trying to update and am seeking the assistance that you offered.

To summarize:
Galaxy version currently 17_09.
Ubuntu 14.04.6
PostgreSQL 9.3.
Python 2.7.6
pip 1.5.4
TLS 1.2
OpenSSL 1.0.1f 6 Jan 2014

As per the instruction - to update I run:
git fetch origin && git checkout release_18.01 && git pull --ff-only origin release_18.01

Output is:
remote: Enumerating objects: 831, done.
remote: Counting objects: 100% (557/557), done.
remote: Total 831 (delta 556), reused 557 (delta 556), pack-reused 274
Receiving objects: 100% (831/831), 450.23 KiB | 0 bytes/s, done.
Resolving deltas: 100% (637/637), completed with 357 local objects.
From GitHub - galaxyproject/galaxy: Data intensive science for everyone.

  • [new branch] dependabot/pip/lib/galaxy/dependencies/python-ldap-3.4.0 → origin/dependabot/pip/lib/galaxy/dependencies/python-ldap-3.4.0
    38a69b1…daa4092 dev → origin/dev
    512526a…5793a1c master → origin/master
    512526a…5793a1c release_21.09 → origin/release_21.09
  • branch release_18.01 → FETCH_HEAD
    Already up-to-date.

Next I run:
./scripts/common_startup.sh

Output is:
Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
SNIMissingWarning
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
InsecurePlatformWarning
Certificate did not match expected hostname: pypi.org. Certificate: {‘notAfter’: ‘Nov 23 18:41:10 2022 GMT’, ‘subjectAltName’: ((‘DNS’, ‘www.python.org’), (‘DNS’, ‘.python.org’), (‘DNS’, ‘docs.python.org’), (‘DNS’, ‘downloads.python.org’), (‘DNS’, ‘pypi.python.org’)), ‘subject’: (((‘commonName’, u’www.python.org’),),)}
Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Collecting MarkupSafe==1.0 (from -r requirements.txt (line 6))
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
SNIMissingWarning
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
InsecurePlatformWarning
Could not fetch URL https://wheels.galaxyproject.org/simple/markupsafe/: There was a problem confirming the ssl certificate: [Errno 1] _ssl.c:510: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol - skipping
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
InsecurePlatformWarning
Certificate did not match expected hostname: pypi.org. Certificate: {‘notAfter’: ‘Nov 23 18:41:10 2022 GMT’, ‘subjectAltName’: ((‘DNS’, ‘www.python.org’), (‘DNS’, '.python.org’), (‘DNS’, ‘docs.python.org’), (‘DNS’, ‘downloads.python.org’), (‘DNS’, ‘pypi.python.org’)), ‘subject’: (((‘commonName’, u’www.python.org’),),)}
Could not fetch URL https://pypi.python.org/simple/markupsafe/: There was a problem confirming the ssl certificate: hostname ‘pypi.org’ doesn’t match either of ‘www.python.org’, ‘.python.org’, ‘docs.python.org’, ‘downloads.python.org’, ‘pypi.python.org’ - skipping
Could not find a version that satisfies the requirement MarkupSafe==1.0 (from -r requirements.txt (line 6)) (from versions: )
No matching distribution found for MarkupSafe==1.0 (from -r requirements.txt (line 6))
/slipstream/galaxy/production/galaxy-dist/.venv/local/lib/python2.7/site-packages/pip/vendor/requests/packages/urllib3/util/ssl.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see Advanced Usage - urllib3 2.0.0.dev0 documentation.
InsecurePlatformWarning
Certificate did not match expected hostname: pypi.org. Certificate: {‘notAfter’: ‘Nov 23 18:41:10 2022 GMT’, ‘subjectAltName’: ((‘DNS’, ‘www.python.org’), (‘DNS’, '.python.org’), (‘DNS’, ‘docs.python.org’), (‘DNS’, ‘downloads.python.org’), (‘DNS’, ‘pypi.python.org’)), ‘subject’: (((‘commonName’, u’www.python.org’),),)}

There seems to be security certificate problems that seem to prevent fetching some python components???

The next steps are:
reboot
(I believe galaxy should start at this point - but it errors)
sh manage_db.sh upgrade -c /slipstream/galaxy/production/config/galaxy.ini
(This works fine and adds database columns)
sh ./scripts/migrate_tools/0011_tools.sh install_dependencies
(This errors - No module named ipaddress)

The galaxy startup log also gives a similar type of error: ImportError: No module named packaging.version

Any help on troubleshooting this would be greatly appreciated. At the moment I cannot update or add any tools. Galaxy has been very helpful for our lab work. Would rather not have to go back to command line data analysis.

12

Hey @MichaelC,

I think you’ll have to update your openssl version, but I’m afraid your ubuntu version has reach the End Of Life In June 2019, I’m not sure you will be able to find more recent versions of OpenSSL for 14.04, and if you do I’m not sure this will be the only problem, as eventually you will also need to upgrade the PostgreSQL version.
My suggestion would be to update ubuntu to a supported version (20.04 is the latest Long Term Support version) and continue the update from there.

13

Thanks for your quick reply!

So - is it possible to upgrade Ubuntu from 14.04 to to 20.04?? From what I have read this is not recommended - instead the suggestion is to do a clean install. If that is true - then I would need to do a new Galaxy install?? Can the Galaxy data be transferred?? I guess there could also be hardware issues with the higher Ubuntu versions.

I also came across this:

which suggests that Ubuntu 14.04 has been extended to 10 years (from 5) to allow users to upgrade (5 year life seems short to me). Could this help??

14

Just in case anyone reads this and is trying to upgrade Galaxy from pre-Galaxy 20 versions (in my case 16) with older pre-Ubuntu 20 versions (in my case 14) )— it is not possible since Galaxy and Ubuntu are co-dependent through this time period. Ubuntu is very difficult/impossible to upgrade successfully. Similarly Galaxy’s requirements (mainly Python) change greatly through this period.

I ended up copying raw data off my Galaxy installation; wiping the server; installing Ubuntu 20; and then the Ansible version of Galaxy 21 – the latter based on these tutorials.

New install of Galaxy

Add on Ansible – install Proftpd

Ansible does make it easy - although there are a couple of errors and poorly explained sections in the tutorials that required some headscratching and tweaking.

Good luck.

3 Likes
15

Hi @MichaelC – Thank you for taking the time to post back your solution!

Btw – Each GTN tutorial has a feedback form at the end. If you have suggestions about how any could be improved, that is definitely welcomed :slight_smile:

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Thanks for the suggestion. Will do…