Modifying dead repository adress

Question: Modifying dead repository adress

2.7 years ago by

uqkjamar • 0

uqkjamar • 0 wrote:

Hello I have a little trouble installing my own tools:

In order to perform MS analysis I'd like to install the tool called msconvert

msconvert :
Repository 'msconvert'
Revision: 3:987d73278bf9 (2015-10-23)

Its dependencies are:

package_proteowizard_3_0_9016
Revision fdc8eb732831
owned by galaxyp

But every time I try to install it go the same error message:

Error downloading from URL https://teamcity.labkey.org/guestAuth/repository/download/bt17/279368:id/pwiz-bin-linux-x86_64-gcc48-release-3_0_9016.tar.bz2
urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)

To understand this problem I've try to download it directly but on my computer I got the same trouble. Then I checked if there was other versions and looked at the xml file related : https://toolshed.g2.bx.psu.edu/repository?repository_id=2b37df05cdf63e2c&changeset_revision=e9ae8f0be737

It's a "new version" and after a try on my computer I had no trouble to download it. But so far I have not succeed to make msconvert work with this new version of the file.

My question is : Is it possible to modify/add/change the actual dependencies of msconverter for the new one ?

If so, how ?

Thanks,

Regards,

Kevin JAMART

software error galaxy • 740 views

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modified 2.7 years ago • written 2.7 years ago by uqkjamar • 0

Thank you for your answer,

But the problem is the only dependency (latest) I can find in the galaxy tool shed is the one with the not working URL. I am on a GVL 4.0. I try to figure out how I can do it manually. If you have any advice I'd gladly follow them.

ADD REPLY • link written 2.7 years ago by uqkjamar • 0

the latest revision of the package_proteowizard_3_0_9016 is https://toolshed.g2.bx.psu.edu/repository?repository_id=2b37df05cdf63e2c&changeset_revision=e9ae8f0be737 and that downloads form https://github.com/bgruening/download_store/raw/master/pwiz/pwiz-bin-linux-x86_64-gcc48-release-3_0_9016.tar.bz2

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by Martin Čech ♦♦ 4.9k

2.7 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

This is probably SSL certificate problem on the side of your host machine, because I can download that file without an issue (as expected from the GitHub domain)

edit: The package should download from this URL, not the one you linked

 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/pwiz/pwiz-bin-linux-x86_64-gcc48-release-3_0_9016.tar.bz2</action>

please try manually uninstalling the package from the Galaxy and installing the latest revision.

btw what version of Galaxy do you have?

ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by Martin Čech ♦♦ 4.9k

2.7 years ago by

uqkjamar • 0

uqkjamar • 0 wrote:

I found how to fix my problem : just remove the 's' from the URL : http[NO S]://teamcity.labkey.org/guestAuth/repository/download/bt17/279368:id/pwiz-bin-linux-x86_64-gcc48-release-3_0_9016.tar.bz2

No certificate problem anymore !

Still no clue why this error happened

ADD COMMENT • link written 2.7 years ago by uqkjamar • 0

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