Question: Data manager failure to create index(s) in 17.05 local
0
gravatar for eklem
9 months ago by
eklem0
eklem0 wrote:

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'

datamanagers admin local 17.05 • 242 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson24k • written 9 months ago by eklem0

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.

ADD REPLYlink written 9 months ago by eklem0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Around the time this question was asked, certain data managers had a problem with dependency installation. Specifically, before running the indexes for a tool suite, that tool suite needed to be installed first. That problem has since been resolved.

The other tool issues were also likely related the 17.05, 17.09, and many Tool Shed repository changes with respect to dependency resolution and installation.

If anyone should run into this type of problem now, troubleshooting help is here: http://galaxy-lib.readthedocs.io/en/latest/topics/dependency_resolution.html

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 78 users visited in the last hour