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/upload.py", line 425, in <module> __main__() File "/home/lun/galaxy-dev/tools/data_source/upload.py", line 413, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/lun/galaxy-dev/tools/data_source/upload.py", 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/binary.py", line 295, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/lun/galaxy-dev/lib/galaxy/datatypes/binary.py", 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.
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:
Which one should I choose? What's the difference between these?