biobakery/MetaPhlAn

[BUG] bowtie database not found

bernt-matthias opened this issue · 1 comments

Describe the bug

I'm getting

No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db

when calling metaphlan as follows:

metaphlan ... --bowtie2db '/gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/' --index 'mpa_v30_CHOCOPhlAn_201901' ...

The folder content is tree /gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/

/gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/
├── mpa_v30_CHOCOPhlAn_201901.1.bt2
├── mpa_v30_CHOCOPhlAn_201901.2.bt2
├── mpa_v30_CHOCOPhlAn_201901.3.bt2
├── mpa_v30_CHOCOPhlAn_201901.4.bt2
├── mpa_v30_CHOCOPhlAn_201901.fna.bz2
├── mpa_v30_CHOCOPhlAn_201901.md5
├── mpa_v30_CHOCOPhlAn_201901.pkl
├── mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
├── mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
└── mpa_v30_CHOCOPhlAn_201901.tar

I guess this is because

if glob(os.path.join(bowtie2_db, "{}*.{}".format(index, bt2_ext))):
only checks if mpa_v30_CHOCOPhlAn_201901.bt2 is available and irgnores the possibility of mpa_v30_CHOCOPhlAn_201901.1.bt2.

Or do the bowtie indices be constructed in a different way?

To Reproduce

See above

Screenshots
If applicable, add screenshots to help explain your problem.

Platform (please complete the following information):

This is for the latest Galaxy tool version

Additional context
NA

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.