FROGS status with recent version of external tools

geraldinepascal / FROGS

FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.

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FROGS status with recent version of external tools #48

Open EricDeveaud opened 4 years ago

EricDeveaud commented 4 years ago

Hello,

some external dependencies of FROGS are available in upper versions than the one documented in the README file, maybee it worth an update of the README file

eg: RDP Classifier is 2.10.2 see https://github.com/rdpstaff/classifier/archive/2.10.2.tar.gz cutadapt is 2.10 see https://github.com/marcelm/cutadapt/archive/v2.10.tar.gz ITSx is 1.1.2 https://microbiology.se/sw/ITSx_1.1.2.tar.gz blast+ is 2.10 see https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ mafft is 7.450 (satbel) or 7.467 (experiemntal) see https://mafft.cbrc.jp/alignment/software/ FastTree is 2.1.11 see http://www.microbesonline.org/fasttree/#Install

would FROGS run with all external dependencies set to the last available version ? including vsearch/2.14.2, swarm/3.0.0

regards

Eric

mariabernard commented 4 years ago

Hello,

Yes we know that. We are working on the FROGS 3.2 release (it makes more time than we thought, also because of covid). This release will take into account dependencies updates, and python3 (and additionnal functionnalities).

In fact RDPClassifier 2.O.2 is not "installable" anymore, you absolutly need to update to 2.0.3 (I publish the conda receipt for it).

But thanks for the remind.

Regards

Maria

EricDeveaud commented 4 years ago

Hello

FYI FROGS-3.1.0 test suite ran successfully with the following tools version

vsearch/2.14.2 
FLASH/1.2.11 
cutadapt/2.10 
swarm/3.0.0 
hmmer/3.3 
ITSx/1.1.2 
blast+/2.10.0 
rdp_classifier/2.12 
EMBOSS/6.6.0 
mafft/7.453 
FastTree/2.1.11 
R/3.6.2

using Python/2.7.17 perl/5.30.1 R/3.6.2

mariabernard commented 4 years ago

Thanks Eric !

Two questions:

where did you find rdp classifier 2.12? last version of rdptools is 2.0.3, and version of classifier is 2.10.2
what tests did you perform ? our test/test.sh script ? The goal of this script is mainly to test that all dependencies are installed but it do not check the results against expected values. This could be done through the tests sections from the Galaxy wrappers, and in these cases there are some differences (at least for vsearch).

But thanks for your return

EricDeveaud commented 4 years ago

rdp_classifier: https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.12.zip

and yes I ran the test/tes.sh script with provided data

I will check the Galaxy wrappers but I guess that outside of galaxy this is a no go ;-)