galaxy on server

Question: galaxy on server

3.5 years ago by

Canada

ajmaninisha • 30 wrote:

Hi,

we recently installed galaxy on our server with proper tool dependencies etc. WHENEVER i try to run my files for some files it gives me output, for others it gives me an error a red symbol showing empty dataset but when i actually opened the output it had all the results.

Why is it happening?

Nisha

no files output • 953 views

ADD COMMENT • link •

modified 3.5 years ago by Martin Čech ♦♦ 4.9k • written 3.5 years ago by ajmaninisha • 30

Could you please add the error message. Thanks!

ADD REPLY • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

please find the snapshot of errors. Kindly advice whenever i want to report the error, it shows mail is not configured for this galaxy instance. See it is giving an error but on the other hand it is displaying the results as well

please check my id: s.good@uwinnipeg.ca

ADD REPLY • link written 3.5 years ago by ajmaninisha • 30

You did not include the error trace or log and we do not have access to your Galaxy. We can't help you if you don't provide more specific problem report.

ADD REPLY • link written 3.5 years ago by Martin Čech ♦♦ 4.9k

Traceback (most recent call last): File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy/lib/galaxy/jobs/init.py", line 1127, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 268, in set_meta proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

ADD REPLY • link modified 3.5 years ago by Martin Čech ♦♦ 4.9k • written 3.5 years ago by ajmaninisha • 30

also i have deleted the datasets from the server but still the memory allocation remains unchanged. kINDLY ADVISE

ADD REPLY • link written 3.5 years ago by ajmaninisha • 30

3.5 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

This is most probably caused by missing samtools on the machine that runs Galaxy. I think the preferred version is 0.1.19

Details on dependencies: https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

ADD COMMENT • link written 3.5 years ago by Martin Čech ♦♦ 4.9k

Ok I will update the Sam tools and then will check again also advise I have deleted several files from my server but the memory quota remains unchanged

ADD REPLY • link written 3.5 years ago by ajmaninisha • 30

Please create a new question with problems regarding quota.

ADD REPLY • link written 3.5 years ago by Martin Čech ♦♦ 4.9k

Similar posts • Search »