ftp.ncbi.nih.gov.primary.assembly.assembled_chromosomes

#!/bin/sh

comment="NCBI mouse assembly Build 39"
# This will be used in the naming the log file
#
# set path of files on remote server
REMOTE_SITE=ftp.ncbi.nih.gov
#url to remote site
REMOTE_SITE_URL=ftp://$REMOTE_SITE
REMOTE_DIR=/genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38/Primary_Assembly/assembled_chromosomes/FASTA/
REMOTE_DIR=/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/GCA_000001635.9_GRCm39_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
LOCAL_DIR=$REMOTE_SITE/genomes/M_musculus_Build39
##if not set, local_dir will be relative to /data/downloads/
## otherwise local_dir is absolute
## 
##loca_dir_is_absolute=0 
#
## List of files to download
#
REMOTE_FILES="*.fna.gz"
#
#wget options
#
WGET_OPTIONS="--no-parent -S -t 10 -nd -m"

#
# wget
# -S = print the headers sent by HTTP servers and responses sent by FTP servers.
# -o = full path to log file
# -O = full path to output file
# -t = number of retries
# -r = reverse
# -k 7 = sort by the 7th column
# -nd = don't create directories
# -m = Turn on options suitable for mirroring. This option turns on recursion 
#    and time-stamping, sets infinite recursion depth and keeps FTP 
#    directory listings. It is currently equivalent to .-r -N -l 
#    inf --no-remove-listing.. 

#******** Optional *************
# Do not download any files if local directories do not exist
local_dir_check=true
# Remove any files in local directory that are not in remote directory
do_deletes=false