Update wget in get_pdb to 1.25.0

[RZ9082]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
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Not sure about versioning. Should we keep it like this or take the wget version? also should we add a suffix?

[bgruening]

.. WARNING: Missing shed metadata field [homepage_url] for repository

Do we have a hypothesis why the old wget is failing now? Is that because of the container?

[RZ9082]

.. WARNING: Missing shed metadata field [homepage_url] for repository

Do we have a hypothesis why the old wget is failing now? Is that because of the container?

@mira-miracoli found the issue, the container has no DNS resolver configuration.

@bgruening should the old container be fixed?

[bgruening]

With a lot of time I would say we should fix the old container. But... I'm fine with shipping this. However are we sure this new container works with singularity? @RZ9082 can you test the old version in docker please. Just ran planemo --biocontainers on the master branch

[mira-miracoli]

With a lot of time I would say we should fix the old container. But... I'm fine with shipping this. However are we sure this new container works with singularity? @RZ9082 can you test the old version in docker please. Just ran planemo --biocontainers on the master branch

I tested with docker and that works indeed, docker is mounting my laptop's resolv.conf.
Singularity complains that the container has no target /etc/resolv.conf and it can therefore not mount it.

[bgruening]

@mira-miracoli https://github.com/galaxyproject/usegalaxy-playbook/blob/727412ca8eb6090ab713b6dff08398802c981ef3/env/common/templates/galaxy/config/tpv/tools.yaml.j2#L2642

[mira-miracoli]

We can try, but I don't really understand how this should solve it:
https://github.com/galaxyproject/usegalaxy-playbook/blob/727412ca8eb6090ab713b6dff08398802c981ef3/env/common/templates/galaxy/config/tpv/tools.yaml.j2#L105-L113

[bgruening]

No idea, I was expecting mounting in the /etc/resolve.conf and not ssl ... but it seems to work for Nate? Maybe ask him?