Question: fail to upload BAM file
gravatar for atcglj
22 months ago by
atcglj10 wrote:

Hello, I have the samtools and bamtools installed in my local galaxy. But this error below was always reported while I was uploading BAM files.

Traceback (most recent call last): File "/home/lun/galaxy-dev/tools/data_source/", line 425, in <module> __main__() File "/home/lun/galaxy-dev/tools/data_source/", line 413, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/lun/galaxy-dev/tools/data_source/", line 340, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/lun/galaxy-dev/lib/galaxy/datatypes/", line 295, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/lun/galaxy-dev/lib/galaxy/datatypes/", line 244, in _get_samtools_version raise Exception(message) Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.

bam • 661 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by atcglj10

I found my Samtools located in /home/lun/galaxy-dev/database/dependencies/samtools, as well as my Picard and Bamtools. I got all these tools from the Galaxy Main tool Shed automatically in the Admin page of my local Galaxy. Is this fold the Galaxy user's path?

I found that there are so many samtools in the Tool Shed. For example:

  1. package_samtools_0_1_18 Tool dependency definition
  2. suite_samtools_0_1_18 Repository suite definition

Which one should I choose? What's the difference between these?

ADD REPLYlink modified 22 months ago • written 22 months ago by atcglj10
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Check to see if the Samtools you have already installed is in your $PATH and add it if needed. Then restart Galaxy and Upload should work.

How to check and add this is in several prior posts, including these two:

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k
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