On Thu, Apr 4, 2013 at 7:19 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: > Hi Peter, > > What is the test error given when you do have a value defined for name in > output? > > > Can you try using 'empty_file.dat'? > > e.g. > > <output name="out_file" file="empty_file.dat" > > > or > > <output name="out_file" file="empty_file.dat" compare="contains"> > > etc
Hi Daniel, That seems to help (plus fixing a typo in one of my child file extensions). However there is something else amiss, but my Galaxy is a little out of date: -------------------- >> begin captured logging << -------------------- galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/user/logout galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9486/ galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.jobs.manager: DEBUG: (1) Job assigned to handler 'main' galaxy.jobs: DEBUG: (1) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/1 galaxy.jobs.handler: DEBUG: dispatching job 1 to local runner galaxy.jobs.handler: INFO: (1) Job dispatched galaxy.jobs.runners.local: DEBUG: Local runner: starting job 1 galaxy.jobs.runners.local: DEBUG: executing: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpOBsw3s/database/tmp/tmpshAqc4 /tmp/tmpOBsw3s/database/tmp/tmpjPyydZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpOBsw3s/database/files/000/dataset_1.dat galaxy.jobs.runners.local: DEBUG: execution finished: python /mnt/galaxy/galaxy-central/tools/data_source/upload.py /mnt/galaxy/galaxy-central /tmp/tmpOBsw3s/database/tmp/tmpshAqc4 /tmp/tmpOBsw3s/database/tmp/tmpjPyydZ 1:/mnt/galaxy/galaxy-central/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpOBsw3s/database/files/000/dataset_1.dat galaxy.jobs: DEBUG: Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs: DEBUG: job 1 ended galaxy.jobs.manager: DEBUG: (2) Job assigned to handler 'main' galaxy.jobs: DEBUG: (2) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/2 galaxy.jobs.handler: DEBUG: dispatching job 2 to local runner galaxy.jobs.handler: INFO: (2) Job dispatched galaxy.jobs.runners.local: DEBUG: Local runner: starting job 2 galaxy.jobs.runners.local: DEBUG: executing: makeblastdb -version &> /tmp/tmpOBsw3s/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out "/tmp/tmpOBsw3s/database/files/000/dataset_2_files/blastdb" -in " /tmp/tmpOBsw3s/database/files/000/dataset_1.dat /tmp/tmpOBsw3s/database/files/000/dataset_1.dat " -title "Just 4 human proteins" -dbtype prot galaxy.jobs.runners.local: DEBUG: execution finished: makeblastdb -version &> /tmp/tmpOBsw3s/database/tmp/GALAXY_VERSION_STRING_2; makeblastdb -out "/tmp/tmpOBsw3s/database/files/000/dataset_2_files/blastdb" -in " /tmp/tmpOBsw3s/database/files/000/dataset_1.dat /tmp/tmpOBsw3s/database/files/000/dataset_1.dat " -title "Just 4 human proteins" -dbtype prot galaxy.tools: DEBUG: Error opening galaxy.json file: [Errno 2] No such file or directory: '/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/galaxy.json' galaxy.jobs: DEBUG: job 2 ended base.twilltestcase: INFO: ## files diff /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd (51 bytes, 4 lines) and /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd (33 bytes, 1 lines) base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 1 is '1111718449\x022\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 2 is '2924903341\x020\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 3 is '3666588750\x021\n' base.twilltestcase: INFO: ## file /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd line 4 is '539247318\x023\n' base.twilltestcase: INFO: ## file /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd line 1 is 'This is a BLAST protein database.' base.twilltestcase: INFO: ## sibling files to /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd in same directory: base.twilltestcase: INFO: ## sibling file: tmpUMWHqD base.twilltestcase: INFO: ## sibling file: twilltestcase-MDnhZ1.html base.twilltestcase: INFO: ## sibling file: twilltestcase-_vAVc9.html base.twilltestcase: INFO: ## sibling file: tmpyiy0Kvempty_file.dat base.twilltestcase: INFO: ## sibling file: twilltestcase-MHWm9w.html base.twilltestcase: INFO: ## sibling file: tmpPaxnAGblastdb.phd base.twilltestcase: INFO: ## sibling file: twilltestcase-dVKyqw.html base.twilltestcase: INFO: ## sibling file: tmpshAqc4 base.twilltestcase: INFO: ## files diff on /mnt/galaxy/galaxy-central/test-data/four_human_proteins.fasta.phd and /tmp/tmpOBsw3s/database/tmp/tmpPaxnAGblastdb.phd lines_diff=0, found diff = 5 --------------------- >> end captured logging << --------------------- As you might guess I've added some additional logging, and it seems that for the blastdb.phd file expected to be produced, the comparison is being made using the default blastdbp datatype's peep text, one line: "This is a BLAST protein database." According to the command being run, the output files should all be named: /tmp/tmpHxY3vf/database/files/000/dataset_2_files/blastdb.p* e.g. /tmp/tmpHxY3vf/database/files/000/dataset_2_files/blastdb.phd Somehow instead the test code is using an altogether different path, and this folder only contains one file with blastdb in its name, and not as the filename alone but munged onto a temp prefix. This seems to be a problem in collecting the output for a composite data type. Another oddity is my input FASTA file is being used twice on the command line (a possible problem testing with a <repeat> <param> perhaps?), note: makeblastdb -out "/tmp/tmpOBsw3s/database/files/000/dataset_2_files/blastdb" -in " /tmp/tmpOBsw3s/database/files/000/dataset_1.dat /tmp/tmpOBsw3s/database/files/000/dataset_1.dat " -title "Just 4 human proteins" -dbtype prot I will have to checkout the latest Galaxy code and retest in case this is something already fixed... Thanks, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
