Re: [galaxy-dev] Strange Could not moveŠ. error
Iry, This is probably an issue with using the from_work_dir attribute. Prior to changeset 524cfb8ca67d, the attribute didn't work when set_metadata_externally was True; 524cfb8ca67d modified the attribute implementation so that it works regardless of how metadata is set. This changeset is not in the most recent distribution, so you'll need to pull from -central if you want to use it immediately. Best, J. On Aug 2, 2012, at 12:24 PM, Iry Witham wrote: Hi Dev-Team, I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server. I have a tool that runs fine on my test instance and fails on my development instance. The servers are identically configured and running the same build. The handler.log from the successful instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689 galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files The same log from the failing instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_131.dat --ref /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_132.dat --genome-size 2716965481
Re: [galaxy-dev] Strange Could not moveŠ. error
Hi Scott, I am running SUSE Linux Enterprise Server 11 SP1 (x86_64) - Kernel \r (\l) on both servers. These are VM's with identical configurations. I know that shutil.move is a python function, but I am not really sure how it works. I appreciate the assistance. Iry From: Scott McManus scottmcma...@gatech.edumailto:scottmcma...@gatech.edu Date: Thursday, August 2, 2012 12:59 PM To: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Strange Could not moveŠ. error Hi Iry- A call to shutil.move is failing, and this could be because file-copying semantics are different on your test instance's OS and/or filesystem than they are on your development instance's OS and/or filesystem. What OS and file system are you using on each? We can also try writing a small Python script to see if shutil.move is failing when copying files from a similar source directory to a similar destination directory. Let me know and I'll be glad to give you a hand. -Scott Hi Dev-Team, I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server. I have a tool that runs fine on my test instance and fails on my development instance. The servers are identically configured and running the same build. The handler.log from the successful instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689 galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files The same log from the failing instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner
Re: [galaxy-dev] Strange Could not moveŠ. error
Ok - that makes sense. So the from_work_dir attribute is part of the tool's data element under outputs, and Jeremy fixed a timing issue. Thanks, Jeremy! -Scott - Original Message - Iry, This is probably an issue with using the from_work_dir attribute. Prior to changeset 524cfb8ca67d, the attribute didn't work when set_metadata_externally was True; 524cfb8ca67d modified the attribute implementation so that it works regardless of how metadata is set. This changeset is not in the most recent distribution, so you'll need to pull from -central if you want to use it immediately. Best, J. On Aug 2, 2012, at 12:24 PM, Iry Witham wrote: Hi Dev-Team, I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server. I have a tool that runs fine on my test instance and fails on my development instance. The servers are identically configured and running the same build. The handler.log from the successful instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689 galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files The same log from the failing instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test
