pleaase provide comprehensive list of dependencies

[EricDeveaud]

Hello, some dfast dependencies are docuemented here: software-distribution.

but while looking at Dockerfile, and one can see that Plasmidfinder and kma are installed

furthermore default-config seems to be abble to use rnammer, genemark and ghostz (in place of ghostx)

some code piece mention other tools eg diamond

also can you point the origin of rpsbproc, as recent ones from the ncbi blast+ distribution are not compatible.

NB recent rpsbproc (from blast+/2.16.0 distribution) can be used with a simple patch changes to dfc/tools/rpsbproc.py

    VERSION_CHECK_CMD = ["rpsbproc", "-version"]
    VERSION_PATTERN = r"rpsbproc: ([\d\.]+)\n"

regards

Eric

[nigyta]

The list of the software dependencies is for those included in the software distribution (under bin directory). They are required when running DFAST with the default setting. DFAST can use rnammer, genemark as an option, but they are not included i nthe software package, so they are missing in the list.

As for rpsbproc, I understand the latest version is not compatible with DFAST. I want to update it to the latest version. However, since the rpsbproc binary for Mac is no longer available, I still stick to the old version. I may give up on supporting Mac in the future. Then, I'm going to update it. The rpsbproc DFAST currently uses was compiled from the source code.

[EricDeveaud]

thanks for the answer.

I use dfast_core with the last rpbsproc (from blast+/2.16.0) with the above mentionned version detection change. it works as expected. reason: our policy is to install stuff from source, and avoid when possible binaries

NB currently running dfast_core withe the following modules loaded:

Python/3.8.1 
hmmer/3.4 
barrnap/0.9 
aragorn/1.2.41 
ghostx/1.3.7 
last/1389 
blast+/2.16.0 
tRNAscan-SE/2.0.12 
graalvm/ce-java19-22.3.1
 MetaGeneAnnotator/2008-8-19 
 PlasmidFinder/2.1.1

NB I'll give a try to compiling rpbsproc on mac. not sure I will succed ;-) NB2 maybee check rpsbproc availability fom macports or brew ?

regards

Eric