Open EricDeveaud opened 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
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
Thanks Eric !
Two questions:
But thanks for your return
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 ;-)
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.gzcutadapt
is 2.10 see https://github.com/marcelm/cutadapt/archive/v2.10.tar.gzITSx
is 1.1.2 https://microbiology.se/sw/ITSx_1.1.2.tar.gzblast+
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/#Installwould FROGS run with all external dependencies set to the last available version ? including vsearch/2.14.2, swarm/3.0.0
regards
Eric