I have created a local Galaxy server and have come across a problem when using mergesamfile, this does not happen when I use the online server.
Tool execution generated the following error message:
Fatal error: Exit code 127 ()
/home/osboxes/galaxy/database/job_working_directory/000/13/galaxy_13.sh: 21: /home/osboxes/galaxy/database/job_working_directory/000/13/galaxy_13.sh: java: not found [bam_header_read] bgzf_check_EOF: Invalid argument
The tool produced the following additional output:
[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
Any suggestions, before i pull all my remaining hair out?