Question: tool_dependency_dir setting not respected?
0
gravatar for danielfortin86
2.7 years ago by
United States
danielfortin86110 wrote:

Hi,

In my "galaxy.ini" file I set:

tool_dependency_dir = /opt/galaxy/shed_tools

 

After a reboot when I try to install the "BLAST" tool from the repository I get an error where it says the location it's trying to install is here:

/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/edward-kirton/blast/f3ac34855f5e/blast

This seems to be the case for any tool I attempt to install.

Is my "tool_dependency_dir" setting not being respected (a bug) or am I doing something else wrong?

I'm running v15.07

 

Thanks!

 

ADD COMMENTlink modified 2.7 years ago by Dave B.410 • written 2.7 years ago by danielfortin86110

Hello,

If you upgrade to release 15.10, does that resolve the path problem? 

The tool shed is intended to be at the same directory level as the Galaxy install by default, although other locations can be specified. Actually nested within the Galaxy install directory may be problemtic, but our team will review. 

I'll post back a Github issue link if it is needed. This would be after I hear back that the upgrade does not resolve the issue (from you) or the dev team jumps in with help.

Thanks for reporting the problem, Jen, Galaxy team

ADD REPLYlink written 2.7 years ago by Jennifer Hillman Jackson25k

No, an upgrade to v15.10 doesn't seem to resolve this problem

ADD REPLYlink written 2.7 years ago by danielfortin86110
2
gravatar for Dave B.
2.7 years ago by
Dave B.410
United States
Dave B.410 wrote:

Yes, the behavior you are observing is correct. There are two paths involved in this situation:

The tool_dependency_dir configuration option is where tool dependencies (e.g. executable files, scripts, etc) are saved. This option is set in galaxy.ini, and contains the directory structure /tool/dependency/dir/{dependency name}/{version}/{repository owner}/{repository name}/{installed revision}

The tool_path option is set in shed_tool_conf.xml, tool_conf.xml, and migrated_tools_conf.xml. This path contains the repositories that you installed, with the path structure /shed/tool/path/{toolshed}/repos/{repository owner}/{repository name}/{installed revision}/{repository name}

The location described in your report is the latter structure, and you should see the data you're expecting if you check the former directory structure.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Dave B.410

Got it! Thanks!!

ADD REPLYlink written 2.7 years ago by danielfortin86110
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