Skip to content

GitLab

Commit fea44e90 authored by vmarques's avatar vmarques
Browse files

Update build_bdr.sh for latest snapshot of EMBL

parent e86e67df
Hide whitespace changes
Inline Side-by-side
build_bdr.sh
View file @ fea44e90
...@@ -38,7 +38,7 @@ source ./config.sh ...@@ -38,7 +38,7 @@ source ./config.sh
## download the sequences ## download the sequences
mkdir EMBL mkdir EMBL
cd 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 * gzip -d *
cd .. cd ..
## download taxonomy ## download taxonomy
...@@ -59,7 +59,7 @@ else ...@@ -59,7 +59,7 @@ else
fi fi
## format the data ## 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 ## ecoPCR to simulate an in silico PCR
#### 50 :: change to 20 : lost of lamproie #### 50 :: change to 20 : lost of lamproie
ecoPCR -d "${rd_prefix}" -e "${ecoPCR_e}" -l "${ecoPCR_l}" -L "${ecoPCR_L}" "${primer5}" "${primer3}" > v_"${rd_prefix}".ecopcr ecoPCR -d "${rd_prefix}" -e "${ecoPCR_e}" -l "${ecoPCR_l}" -L "${ecoPCR_L}" "${primer5}" "${primer3}" > v_"${rd_prefix}".ecopcr
......
Supports Markdown
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