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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Metaphlan2 fails #21

Closed ehj000 closed 3 years ago

ehj000 commented 3 years ago

I suspect this is because the database the tool use is downloaded first time the tool is used. Can someone with ssh access try to run this command to download the database:

metaphlan2.py --install

torfinnnome commented 3 years ago

It looks like the database is managed using a data manager:

From https://github.com/galaxyproject/tools-iuc/blob/master/tools/metaphlan2/repository_dependencies.xml: "This requires the MetaPhlAn2 data manager definition to install all required databases."

ehj000 commented 3 years ago

Ok, but using the data manager gives the following error:

/bin/sh: download_metaphlan2_db.py: command not found Traceback (most recent call last): File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_metaphlan2_database_downloader/9c4ad82be5bd/data_manager_metaphlan2_database_downloader/data_manager/data_manager_metaphlan2_download.py", line 144, in target_dir) File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_metaphlan2_database_downloader/9c4ad82be5bd/data_manager_metaphlan2_database_downloader/data_manager/data_manager_metaphlan2_download.py", line 99, in download_metaphlan2_db subprocess.check_call(cmd, shell=True) File "/usr/lib64/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'download_metaphlan2_db.py --output /srv/galaxy/jobs/005/5674/working/dataset_9058_files' returned non-zero exit status 127.

torfinnnome commented 3 years ago

Ok, will look into it.

torfinnnome commented 3 years ago

The requirement seems to be properly defined in the tool xml file, /srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_metaphlan2_database_downloader/83f07f40b200/data_manager_metaphlan2_database_downloader/data_manager/data_manager_metaphlan2_download.xml:

<requirement type="package" version="2.6.0">metaphlan2</requirement>

However, when running the data manager, it is using the default Singularity container. And I really have no idea why. I will try to ask around.

ehj000 commented 3 years ago

I am planning to use Metaphlan2 for to upcoming ELIXIR workshops. Any progress on troubleshooting why the data manager tool is failing? If not, I could try to install the database manually

torfinnnome commented 3 years ago

I was able to install the metaphlan2 database on prod now (I gave up - Galaxy is not ready for a Singularity-only setting, sigh). Could you test your tools/workflow?

ehj000 commented 3 years ago

Looks like it finds the database, but throws another error: WARNING:galaxy.model:Datatype class not found for extension 'biom' In the Data type table, I find Biom1 and Biom2. Anyone that can instruct me how to add a new data type in usegalaxy?

torfinnnome commented 3 years ago

The metahplan2 tool xml from the tool-shed is not in sync with https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/. (Which is weird and annoying.) I have now installed the version from github, which should fix the biom dataclass issue.

However, I need to restart Galaxy in order to make it visible. Will restart when there is less traffic, some time later today.

torfinnnome commented 3 years ago

Seems to work now?

Screenshot 2021-03-10 at 08 22 00
ehj000 commented 3 years ago

Yes, thank you again Torfinn. One note for those that will use this: it requires the input type fastq (and not fastqsanger as many other Galaxy tools)