Question: Issue with Crossmap in local Galaxy instance
gravatar for christopher.previti
16 months ago by
christopher.previti0 wrote:

Dear Galaxy users and developers,

I installed the tool CrossMap in our local Galaxy instance and I am getting following error:

Traceback (most recent call last): File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/", line 170, in prepare_job job_wrapper.prepare() File "/opt/galaxy/galaxy/lib/galaxy/jobs/", line 864, in prepare self.command_line, self.extra_filenames, self.environment_variables = File "/opt/galaxy/galaxy/lib/galaxy/tools/", line 454, in build raise e NotFound: cannot find 'replace' while searching for 'replace'

We are running the newest Galaxy version and all CrossMap dependencies seem to be met, at least according to the toolshed.

I would greatly appreciate some suggestions on how to resolve this.

Thanks and best regards, Christopher Previti

ADD COMMENTlink modified 14 months ago • written 16 months ago by christopher.previti0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The tool shows that there are dependency-relationship problems within the Tool Shed for the associated dependency package. See this warning at the top of the tool's page here.

The settings for name, version and type from a contained tool configuration file's requirement tag does not match the information for the following tool dependency definitions in the tool_dependencies.xml file, so these tool dependencies have no relationship with any tools within this repository. * name: python, type: package, version: 2.7.10

You could try installing the dependency package directly (if it was not already installed - it may not have been done automatically). Or, install each dependency directly to see if that resolves the problem. If that doesn't help or seems too tedious, log into the tool shed and send the tool author a message. This particular author is still very active in Galaxy development and will almost certainly get back to you with advice.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson25k
gravatar for y.hoogstrate
14 months ago by
y.hoogstrate460 wrote:

Hi there (and thanks to Jennifer to bring me here).

I knew back then (2015) there were problems with CrossMap (in particular with the installation) and I stopped working on this because I was aware of the upcoming transistion to BioConda. After that transition was completed, I did some updates but instead of updating my repository I had send it to IUC and received a number of updates also from IUC. To my surprise I saw today that IUC's CrossMap version is not yet deployed in the tool sheds so please watch this thread:

I have immediately deprecated my CrossMap repository to avoid further confusion and added a tiny patch to the IUC's one in the hope to release it immediately after approval.

thanks for the alert and all best,


ADD COMMENTlink modified 14 months ago • written 14 months ago by y.hoogstrate460

Thanks again for the update, I got crossmap to install without isssue. Running it works fine if you have a chain file in you history, but if you use local chain files (listed in the liftOver.loc) there is problem with the xml. Currently crossmap doesn't use the build information of the dataset (a bed file could contain hg38 coordinates and it wouldn't know). That means one would have to parse the "dbkey" and "name" columns of the lifOver.loc in order to specify both current build and the one you want to convert to. At the moment there is a select that only allows you to specify which one you want to convert to...leading to multiple instances of hg19, hg18 basically can't indicate which your current build is.

My hack: Change the liftover.loc "name" column: hg19 would be for instance -> hg38_to_hg19 if you want to use the chain file converting hg38 to hg19, you now know where you're coming from and where you want to go.

Hope this helps, I know there are probably many better ways of doing it.

Cheers, Christopher

ADD REPLYlink written 14 months ago by christopher.previti0

I get the point, thanks. I will take a look at this, I am quite certain this is possible :)

ADD REPLYlink written 13 months ago by y.hoogstrate460

This issue has been resolved in the latest revision of crossmap. Could you confirm this?

ADD REPLYlink written 13 months ago by y.hoogstrate460
gravatar for christopher.previti
14 months ago by
christopher.previti0 wrote:

Thanks everybody :) I hate to cross-post...but any idea how to get Crossmap (or any other program) to stop "installing". I had another issue, where the installation monitor in the admin interface shows (in this case) Crossmap as installing, but the status is basically frozen and doesn't go away after a restart. Jen gave me some tips in my original post...

Any ideas for a quick fix? I'll copy any answers to the above post...

Cheers, Christopher

ADD COMMENTlink written 14 months ago by christopher.previti0
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