V12?

[ccgallen]

Hi Yanbin,

To use the version 12 databases can I simply change all the V11 to V12 here?

test -d db || mkdir db
cd db \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/fam-substrate-mapping-08252022.tsv \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/PUL.faa && makeblastdb -in PUL.faa -dbtype prot \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL_07-01-2022.xlsx \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL_07-01-2022.txt \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL.tar.gz && tar xvf dbCAN-PUL.tar.gz \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm && hmmpress dbCAN_sub.hmm \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fa && diamond makedb --in CAZyDB.08062022.fa -d CAZy \
    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/dbCAN-HMMdb-V11.txt && mv dbCAN-HMMdb-V11.txt dbCAN.txt && hmmpress dbCAN.txt \
    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/tcdb.fa && diamond makedb --in tcdb.fa -d tcdb \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/tf-1.hmm && hmmpress tf-1.hmm \
    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/tf-2.hmm && hmmpress tf-2.hmm \
    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/stp.hmm && hmmpress stp.hmm \
    && cd ../ && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.fna \
    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.faa \
    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.gff

[yinlabniu]

We updated CAZyDB fasta file (https://bcb.unl.edu/dbCAN2/download/Databases/V12/CAZyDB.07262023.fa) and dbCAN HMM file (https://bcb.unl.edu/dbCAN2/download/Databases/V12/dbCAN-HMMdb-V12.txt), so just change the two files for wget would be file.

Yanbin

[ccgallen]

Thanks!