mpa_v30_CHOCOPhlAn_201901 missing (but mpa_v31_CHOCOPhlAn_201901 present instead)

$ metaphlan --version
MetaPhlAn version 3.0.7 (09 Dec 2020)
$ humann --version
humann v3.0.0.alpha.4
$ biobakery_workflows --version
biobakery_workflows v3.0.0-alpha.7

When attempting to run:

biobakery_workflows_databases --install wmgx

according to: Installing the workflows with pip · biobakery/biobakery_workflows Wiki · GitHub

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

indeed the step:

metaphlan --install --nproc 2

does not download the version 30 of the DB but only the 31 as you can see from:

$ metaphlan --install --nproc 2

Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 31507.69 %  55.54 MB/sec  0 min -0 sec         
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.tar
Downloading file of size: 407.85 MB
Building a SMALL index85 MB/sec  0 min  0 sec         
407.85 MB 100.00 %   2.85 MB/sec  0 min  0 sec         
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.md5
Downloading file of size: 0.00 MB
0.01 MB 12800.00 %  186.18 MB/sec  0 min -0 sec         

Decompressing /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna.bz2 into /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna

Building Bowtie2 indexes
Removing uncompress database /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_v31_CHOCOPhlAn_201901.fna

Download complete
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? Or should I do a manual download from Index of /biobakery3/metaphlan_databases?

Thanks,

RD

The issue is with biobakery_workflows_databases.py and shotgun.py that have the version of the metaphlan_databases hardcoded, a solution would be to read the version from /PATH/TO/biobakery/lib/python3.6/site-packages/metaphlan/metaphlan_databases/mpa_latest:

$ grep -R metaphlan /u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/* | grep 30
/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/biobakery_workflows_databases.py:        strainphlan_db=os.path.join(os.path.dirname(metaphlan.__file__),"metaphlan_databases","mpa_v30_CHOCOPhlAn_201901")
/u/local/apps/PYTHON-VIRT-ENVS/3.6.8/biobakery/lib/python3.6/site-packages/biobakery_workflows/tasks/shotgun.py:                strainphlan_pkl=os.path.join(os.path.dirname(metaphlan.__file__),"metaphlan_databases","mpa_v30_CHOCOPhlAn_201901.pkl")