anvi-setup-pfams does not handle already downloaded local file

[EricDeveaud]

Short description of the problem

despite the anvi-setup-pfams help says This program by default attempts to use previously downloaded files in your Pfam data directory if there are any. anvi-setup-pfams does not handle this possibility does not handle already downloaded files

anvi'o version

maestro-builder:PlasX/PlasX-0.1 > anvi-self-test --version
Anvi'o .......................................: hope (v7)

Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1

System info

maestro-builder:PlasX/0.1 > cat /etc/os-release 
NAME="CentOS Linux"
VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-8"
CENTOS_MANTISBT_PROJECT_VERSION="8"

anvio installed in a virtualenv

Detailed description of the issue

expected is that anvi-setup-pfams takes in account previously downloaded pfam files and not tries to downlaod it again. this is not possible on our cluster setup where compute nnodes does nnot have access to internet. I would expect to be abble to downlaod the required pfam files and let anvi-setup-pfams process it.

Files to reproduce

lets say I want to use pfam v32.

mkdir ~/Pfam_v32 && cd ~/Pfam_v32/
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam.version.gz
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.clans.tsv.gz
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/md5_checksums
anvi-setup-pfams --pfam-data-dir ~/Pfam_v32/ --pfam-version 32.0

regards

Eric

[meren]

Solved via #1942, but let's keep the issue open until one more person has a chance to test it.

[ivagljiva]

It's been over a year and nobody else has come here to say they are still having this issue, so I am closing it :)