Thanks for the report! I can confirm the bug and I opened a pull request with the fixes here https://github.com/galaxyproject/galaxy/pull/139.
-John On Fri, Apr 17, 2015 at 4:20 AM, Roberto Alonso <roal...@gmail.com> wrote: > Hello, > > I am writing some code to enable parallelization for some tool wrappers. > First, I did it for simple bwa wrapper, but now I am modifying > toolshed.g2.bx.psu.edu/repos/devteam/bwa/c71dd035971e/bwa/bwa-mem.xml to > check if the code would work with this wrapper. So, I wrote some code that I > thing was necessary in order to merge some bam and I added the parallelism > tag (in bold) to the config file: > > <tool id="bwa_mem" name="BWA-MEM" version="0.1"> > > <macros> > <import>bwa_macros.xml</import> > </macros> > > <requirements> > <requirement type="package" > version="0.7.10.039ea20639">bwa</requirement> > <requirement type="package" version="1.1">samtools</requirement> > </requirements> > <description>- map medium and long reads (> 100 bp) against reference > genome</description> > <parallelism method="multi" split_size="3" shared_inputs="ref_file" > split_mode="number_of_parts" merge_outputs="bam_output" > split_inputs="fastq_input1,fastq_input2" ></parallelism> > > > <command> > ... > > So, everything works well, and the resulting bam from parallelization mode > and without the parallelization mode is the same but the Galaxy log throws > an error regarding metadata, it says something like this: > > galaxy.jobs.splitters.multi DEBUG 2015-04-17 09:54:58,335 merge finished: > /home/ralonso/galaxy/database/files/000/dataset_198.dat > galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,473 executing external > set_meta script for job 200: python > /home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py > /home/ralonso/galaxy/database/tmp/tmpHS8Byo > /home/ralonso/galaxy/database/job_working_directory/000/200/galaxy.json > /home/ralonso/galaxy/database/tmp/metadata_in_HistoryDatasetAssociation_198_yOGiQG,/home/ralonso/galaxy/database/tmp/metadata_kwds_HistoryDatasetAssociation_198_nAsQoq,/home/ralonso/galaxy/database/tmp/metadata_out_HistoryDatasetAssociation_198_I_cLs4,/home/ralonso/galaxy/database/tmp/metadata_results_HistoryDatasetAssociation_198_qhjzoV,/home/ralonso/galaxy/database/files/000/dataset_198.dat,/home/ralonso/galaxy/database/tmp/metadata_override_HistoryDatasetAssociation_198_ScKLqH > Traceback (most recent call last): > File "/home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py", line 1, > in <module> > from galaxy_ext.metadata.set_metadata import set_metadata; > set_metadata() > ImportError: No module named galaxy_ext.metadata.set_metadata > galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,624 execution of > external set_meta finished for job 200 > galaxy.datatypes.metadata DEBUG 2015-04-17 09:54:58,714 setting metadata > externally failed for HistoryDatasetAssociation 198: External set_meta() not > called > > When using no parallelization mode, there is no problem, also because Galaxy > doesn't go through this part of code, I mean it doesn't execute this. > I see that Galaxy have to do something with metada attributes, but what is t > trying to do? is there any way to solve this? > > Thank you very much > > Regards, > Roberto > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
