User: christopher.previti

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Posts by christopher.previti

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Comment: C: Issue with Crossmap in local Galaxy instance
... 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 ...
written 8 months ago by christopher.previti0
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Answer: A: Bugfix for bwa_meth data manager
... Oops small correction, it's only the path in the loc file that is wrong, the files themselves are in the right spot. ...
written 8 months ago by christopher.previti0
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Answer: A: Bugfix for bwa_meth data manager
... Ok, I think I got it. I think it was two issues : 1. Bwa mem had to be in the PATH 2. The indices that were generated were not put in their proper place. Below you can see a (badly formatted) part of the loc file. I made an index for the chicken genome: galGal5_PhiX_Lambda galGal5_PhiX_Lambd ...
written 8 months ago by christopher.previti0
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Answer: A: Issue with Crossmap in local Galaxy instance
... 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 afte ...
written 8 months ago by christopher.previti0
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Comment: A: Installing tool "frozen"
... Hi, Yes of course, more information would be helpful: The tool was crossmap which I had to try because l was not able to get lift-over to run (other story): Name: crossmap Owner: yhoogstrate Revision: 9c7cc3690f33 Installation Status: Installing tool dependencies -> this state is basically ...
written 9 months ago by christopher.previti0
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Answer: A: Bugfix for bwa_meth data manager
... Dear Jen and the Galaxy team, This data manager is still throwing an error... Here's the message: Dataset generation errors Dataset 2591: bwa-meth index The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File "/opt/galaxy/ ...
written 9 months ago by christopher.previti0
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Answer: A: Bugfix for bwa_meth data manager
... Thanks for the infos, I'll try it with the updated version. Cheers, Christopher ...
written 9 months ago by christopher.previti0
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Installing tool crossmap results in "frozen" state in local 17.05
... Dear all, I have a rather strange issue with the tool shed installation monitor of our local Galaxy instance. One of the tools that I wanted to install is "frozen" in the "installation" state and can't be removed. I restarted Galaxy but it will not go away. Anybody have advise for me? Cheers, Chris ...
frozen toolshed monitoring crossmap written 9 months ago by christopher.previti0 • updated 8 months ago by Jennifer Hillman Jackson25k
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Bugfix for bwa_meth data manager
... Dear all, I found a bug in the data manager for the making bwa-meth indices. I'm not sure if this is of interest but here goes: Old line 27: data_table_entry = dict(value=args.dbKey, dbkey=args.dbkey, name=args.name, path=args.dbKey) New and corrected: data_table_entry = dict(value=args.dbkey, d ...
bwa-meth bugfix datamanager written 9 months ago by christopher.previti0
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Issue with Crossmap in local Galaxy instance
... 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/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/opt/galaxy/ ...
galaxy software error crossmap written 11 months ago by christopher.previti0

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