Impossible to install Pfam to target location

simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)

GNU General Public License v2.0

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Impossible to install Pfam to target location #35

Open SilasK opened 5 years ago

SilasK commented 5 years ago

Sorry, I'm frustrated after some time debugging Virsorter.

Virsorter depends on a outdated version of Pfam. I can download it but apparently Virsorter requires it to be at /Pfam_27/which I don't have acces.

By the way: MGA can be installed using conda but needs to be renamed.

simroux commented 5 years ago

Hi Silas, Are you trying to run VirSorter through the Docker container or via cloning from GitHub + custom Conda environment ? If the latter, there is an option called "--data-dir" where you can provide a path to a folder including PFAM. This should look something like:

./wrapper_phage_contigs_sorter_iPlant.pl ... your other options ... --data-dir /path/to/dbs/

Then in the folder /path/to/dbs/ VirSorter will expect:

a folder "PFAM_27/" with two files, Pfam-A.hmm and Pfam-B.hmm
the files and folders from "virsorter-data-v2.tar.gz"

SilasK commented 5 years ago

Yea I use virsorter in a conda environment, I specified the datadir where I downloaded the vrsorter data v2.

If I understand the error message correctly virsorter was looking for /Pfam_27 (root/Pfam_27) which is only possible in the docker.

simroux commented 5 years ago

The error message is weird, and doesn't seem to be accurate (sorry). VirSorter expects Pfam to be in the same directory as the virsorter data v2, in its own subfolder called "PFAM_27". Could you test this and check if it works better ?