problems with tools in local galaxy

Question: problems with tools in local galaxy

2.3 years ago by

zhihengbai • 40 wrote:

After clicking the 'Download local tool' button in the admin interface, a blank screen shown up. So I checked the 'View Tool Error Logs'. OK... now the system cannot find a file which is exactly there.(btw the 'home' in the 'files' window is the same path as '/home/visitors/bzh' in the 'browser' window's Error description)

Hope someone has good idea about this

software error • 1.0k views

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modified 2.3 years ago by Martin Čech ♦♦ 4.9k • written 2.3 years ago by zhihengbai • 40

The tool shed is undergoing some upgrades today. This is likely related. Try again later today or wait for our team to post back that it is at full functionality again.

Our apologies for the inconvenience. The changes are urgent. Jen, Galaxy team

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

2.3 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

The functionality indeed seems troublesome - thank you for reporting it.

However even if it worked correctly it seems you do not have any tools installed via the Tool Shed (which is what the feature is for) and you do not have any Tool Sheds configured for your Galaxy. The only tools in your Galaxy should be the ones on the tools/ folder on your filesystem, that come with Galaxy's code.

Have a look at https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to get you started if you want to add tools from the Tool Shed.

edit: as of the .loc file error I am unsure what could that be and will point someone else here to check

ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Martin Čech ♦♦ 4.9k

Thanks for the reply. You are right there was no tool in the tools shed because tools installation was what I was trying to do. It seemed that opening the 'Download local tools' page is a step of installation... btw, I checked the 'Installing Tools into Galaxy from Tool Shed' page before I posted this question and it seemed that the page was outdated (eg. There was no 'Search and browse tool sheds' link to click).

ADD REPLY • link written 2.3 years ago by zhihengbai • 40

The 'Search and Browse' link only appears if you have a Tool Shed configured for your Galaxy, please have a look at the 'Connect Your Galaxy to a custom Tool Shed' section of the mentioned tutorial.

The 'download local tool' feature is used to download a tarball of a local tool isntalled from the Tool Shed - this is a feature generally useful for tool developers or if you run your own Tool Shed.

Btw I have created an issue for the problem you reported here: https://github.com/galaxyproject/galaxy/issues/2722

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Um...but the 'main tools shed' is supposed to be there by default,right? (I've done the 'set the directory for tool dependencies' and 'create and activate tool shed conf file' things) So the 'Search and Browse' link should have been there.

Another question: for those tools not present in the web version galaxy but existing in the 'main tools shed' , is there a way to use them?(eg. I need to convert 'gene bank' file to 'gff' format but the 'geneban2gff' is not present on the webserver)

ADD REPLY • link written 2.3 years ago by zhihengbai • 40

The fact you do not have 'Search Tool Shed' option shown means that you misconfigured it somehow because fresh clone of Galaxy shows it to all admins without any other changes.

I do not understand your second question. What do you mean by 'web version Galaxy'. You use the tools from Tool Shed by installing them into Galaxy and then executing them from the Galaxy.

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

Sorry for the ambiguity. I mean use the free server through the link 'https://usegalaxy.org' rather than locally installing a galaxy. I log in to https://usegalaxy.org and 'geneban2gff' tool is not there, but this tool exists in https://toolshed.g2.bx.psu.edu. So, the question is 'Can I use this tool on the free public server?'

ADD REPLY • link written 2.3 years ago by zhihengbai • 40

I am sorry but that is not possible now. Every Galaxy's toolset is defined by its administrator. And the administrators of usegalaxy.org did not choose that tool to be available on the instance. I will check whether it will be fine to install this tool and let you know.

ADD REPLY • link written 2.3 years ago by Martin Čech ♦♦ 4.9k

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