上传高通量测序原始文件

#!/bin/bash

#set -x
set -e
set -u

usage()
{
cat <<EOF >&2
${txtcyn}
Usage:

$0 options${txtrst}

${bldblu}Function${txtrst}:

This script is used to upload files to an FTP server using lftp.

${txtbld}OPTIONS${txtrst}:
    -f    FTP address ${bldred}[NECESSARY]${txtrst}
    -u    User name ${bldred}[NECESSARY]${txtrst}
    -p    Password ${bldred}[NECESSARY]${txtrst}
    -t    Target dir ${bldred}[NECESSARY]${txtrst}
    -s    Source dir ${bldred}[NECESSARY]${txtrst}    
EOF
}

ftp=
user=
passwd=
target=
source_dir=

while getopts "hf:u:p:t:s:" OPTION
do
    case $OPTION in
        h)
            usage
            exit 1
            ;;
        f)
            ftp=$OPTARG
            ;;
        u)
            user=$OPTARG
            ;;
        p)
            passwd=$OPTARG
            ;;
        t)
            target=$OPTARG
            ;;
        s)
            source_dir=$OPTARG
            ;;
        ?)
            usage
            exit 1
            ;;
    esac
done

if [ -z $ftp ]; then
    usage
    exit 1
fi

cat <<END >lftp.script
open -u ${user},${passwd} ${ftp}
mkdir -p ${target}
cd ${target}
cache size 33554432
set cmd:parallel 10
mput -c ${source_dir}/*
END

lftp -f lftp.script

Receiver: geo@ncbi.nlm.nih.gov

Subject: ftp upload

Context:

Dear Sir/Madam, 

Thanks for you kindly host such great public data resource.

I have successfully transferred my data to NCBI-GEO ftp sever. 

Here is the information you may be needed for further processing

1. GEO account username: 我的GEO用户名
2. Names of the directory and files deposited: 文件上传的路径, 对应上
面的fasp/detination_dir/
3. Public release date: 2018-12-31 文件释放时间，一般可以设置的比较远

If there is any format or content problem,  please do not hesitate to
contact me.

Best, 

Name