Question: Realign_Target_Creator error running
gravatar for abedkurdi10
23 months ago by
abedkurdi100 wrote:

Hi all, I am trying to run realign_target_creator in my local galaxy server and it is producing the following error:

Traceback (most recent call last):
  File "/home/pk2/shed_tools/", line 126, in <module>
    if __name__=="__main__": __main__()
  File "/home/pk2/shed_tools/", line 90, in __main__
    gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
  File "/home/pk2/shed_tools/", line 29, in gatk_filename_from_galaxy
    os.symlink( galaxy_filename, gatk_filename )
OSError: [Errno 17] File exists

Does anyone knows how to solve it ??

I appreciate your help, thank you.

ADD COMMENTlink modified 23 months ago by Jennifer Hillman Jackson25k • written 23 months ago by abedkurdi100
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a much older version of the GATK tool and it has been deprecated (it will not be updated, but is still available). Newer versions of GATK tools in the Tool Shed are recommended as alternatives.

It is also a good idea to make sure your local is running the latest Galaxy version 16.07.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 23 months ago by Jennifer Hillman Jackson25k

Actually, I am running the latest version of Galaxy. I tried to install newer versions of GATK, but there is some dependencies are "refusing" to install so I get "Installed, missing tool dependencies". Is there anyway to solve this ?

the problem is in the following package: "package_r_for_gatk_3_4_0 ". I tried to "repair repository" but it fails. the error output is the following:

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
ERROR: dependency ‘gdata’ is not available for package ‘gplots’
* removing ‘/home/pk2/galaxy/database/dependencies/package_r_for_gatk_3_4_0/’

Thank you very much.

ADD REPLYlink modified 23 months ago • written 23 months ago by abedkurdi100

I suggest writing the tool author through the tool shed about this updated GATK package and the dependencies issues. Log in there, navigate to the tool, then in the upper right corner is a menu with a contact form.

Another option is to use this GATK version instead: Should that also not install or present problems, the IUC authors can be contacted. Please be aware that GATK within Galaxy is only loosely supported now, due to licensing and other factors.

You might want to explore using alternative variant analysis tools. Many can be reviewed at and within the tool shed. Help is here ( plus there are many other tutorials online from various sources (google "galaxy variant calling tutorial").

ADD REPLYlink written 23 months ago by Jennifer Hillman Jackson25k
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