Commit fea44e90 authored by vmarques's avatar vmarques
Browse files

Update build_bdr.sh for latest snapshot of EMBL

parent e86e67df
......@@ -38,7 +38,7 @@ source ./config.sh
## download the sequences
mkdir EMBL
cd EMBL
wget ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/std/*
wget ftp.ebi.ac.uk/pub/databases/ena/sequence/snapshot_latest/std/*
gzip -d *
cd ..
## download taxonomy
......@@ -59,7 +59,7 @@ else
fi
## format the data
obiconvert --skip-on-error --embl -t ./TAXO --ecopcrdb-output="${rd_prefix}" EMBL/rel_std_*.dat
obiconvert --skip-on-error --embl -t ./TAXO --ecopcrdb-output="${rd_prefix}" EMBL/*.dat
## ecoPCR to simulate an in silico PCR
#### 50 :: change to 20 : lost of lamproie
ecoPCR -d "${rd_prefix}" -e "${ecoPCR_e}" -l "${ecoPCR_l}" -L "${ecoPCR_L}" "${primer5}" "${primer3}" > v_"${rd_prefix}".ecopcr
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment