Been having a devil of a time getting Galaxy going on a brand new 17_05 installation.
I have used only main repository valid tools and data managers, and keep running into problems. I have successfully downloaded hg19 (apx 3.0GB file) via the data_manager_fetch_DBKey tool, but then when trying to run either a sam_fasta_index_builder or a bwa-mem_index_builder I get an immediate error.
The web/galaxy interface does not tell you what the error IS, but fortunately it gives you the command line that was attempted... so I copied and pasted it into a terminal on the host machine and got the following:
sysadmin@debian-jessie-galaxy2:~$ python '/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/1f54e98616af/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py' '/home/sysadmin/galaxy-dist/database/files/000/dataset_42.dat' --fasta_filename '/home/sysadmin/galaxy-dist/tool-data/hg19/seq/hg19-DBKey-fetch.fa' --fasta_dbkey 'hg19' --fasta_description 'hg19-DBKey-fetch' --data_table_name fasta_indexes Traceback (most recent call last): File "/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/1f54e98616af/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 92, in <module> main() File "/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/1f54e98616af/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 76, in main os.mkdir( target_directory ) OSError: [Errno 2] No such file or directory: '/home/sysadmin/galaxy-dist/database/job_working_directory/000/37/dataset_42_files'
sysadmin@debian-jessie-galaxy2:~$ python '/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder.py' '/home/sysadmin/galaxy-dist/database/files/000/dataset_43.dat' --fasta_filename '/home/sysadmin/galaxy-dist/tool-data/hg19/seq/hg19-DBKey-fetch.fa' --fasta_dbkey 'hg19' --fasta_description 'hg19-DBKey-fetch' --data_table_name bwa_mem_indexes Traceback (most recent call last): File "/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder.py", line 91, in <module> main() File "/home/sysadmin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder.py", line 73, in main os.mkdir( target_directory ) OSError: [Errno 2] No such file or directory: '/home/sysadmin/galaxy-dist/database/job_working_directory/000/38/dataset_43_files'
Also getting Error code 127's on most of my attempts at tool downloads from the main tool shed repository. BWA, FASTQC, CLUSTALW, etc.
The only things I have gotten to work properly are FASTQ_groomer and FASTQ_to_FASTA conversion which successfully converted an ion torrent fastq file into a fastqsanger and then converted that into a fasta file.