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
> > /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 --p-value 0.001 --bigger-window 1.5
> > --no-annotate --log2-threshold 0.6; cd
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist;
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/set_metadata.sh
> > ./database/files
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
> > . /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/universe_wsgi.ini
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/tmp/tmpgTn7ey
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/galaxy.json
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_in_HistoryDatasetAssociation_136_VYG968,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_kwds_HistoryDatasetAssociation_136_yo_4aK,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_out_HistoryDatasetAssociation_136_D6HwmI,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_results_HistoryDatasetAssociation_136_zunslF,,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_override_HistoryDatasetAssociation_136_FDUxso
> 
> > galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,680 (113) queued
> > in
> > default queue as 112609.scyld.localdomain
> 
> > galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:30,163
> > (113/112609.scyld.localdomain) PBS job state changed from N to R
> 
> > galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298
> > (113/112609.scyld.localdomain) PBS job state changed from R to C
> 
> > galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298
> > (113/112609.scyld.localdomain) PBS job has completed successfully
> 
> > galaxy.jobs DEBUG 2012-08-02 11:54:33,354 finish(): Could not move
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/cnv_seq_result.cnv
> > to
> > /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_140.dat
> > as directed by from_work_dir
> 
> > galaxy.jobs DEBUG 2012-08-02 11:54:33,467 job 113 ended
> 

> > Why would one fail and the other succeed?
> 

> > Thanks,
> 
> > Iry
> 
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