search

biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
Other
97 stars 33 forks source link

mpa_v30_CHOCOPhlAn_201901 missing (but mpa_v31_CHOCOPhlAn_201901 present instead) #32

Closed rdauria closed 1 year ago

rdauria commented 1 year ago

Hello,

While installing the biobakery-workflow dependencies according to https://github.com/biobakery/biobakery_workflows/wiki/Installing-the-workflows-with-pip, during the step:

$ biobakery_workflows_databases --install wmgx

I get:

Could not locate a Bowtie index corresponding to basename "/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901"

looking in /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/ I see the following:

$ ls /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.
mpa_v31_CHOCOPhlAn_201901.1.bt2      mpa_v31_CHOCOPhlAn_201901.3.bt2      mpa_v31_CHOCOPhlAn_201901.fna.bz2    mpa_v31_CHOCOPhlAn_201901.pkl        mpa_v31_CHOCOPhlAn_201901.rev.2.bt2
mpa_v31_CHOCOPhlAn_201901.2.bt2      mpa_v31_CHOCOPhlAn_201901.4.bt2      mpa_v31_CHOCOPhlAn_201901.md5        mpa_v31_CHOCOPhlAn_201901.rev.1.bt2  mpa_v31_CHOCOPhlAn_201901.tar

and if I try to reinstall the DB I get:

$ metaphlan --install --nproc 2 
The database is installed

Is it possible that the metaphian DB has been updated from version 30 to 31 and that biobakery needs to be updated?

Thanks,

RD

github-actions[bot] commented 1 year ago

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.