EDirect在linux和mac下的安裝

edirect是非常有用的工具

其使用要用來perl，mac都預先安裝了perl

安裝的時候最好按下面進行

開啟終端

cd ~
/bin/bash
perl -mnet:
:ftp -e
\ '$ftp
= new net:
:ftp(
"ftp.ncbi.nlm.nih.gov"
, passive =>1)
;$ftp
->login;
$ftp
->binary;
$ftp
->get(
"/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf -
rm edirect.tar.gz
builtin exit
export path=
$path
:$home
/edirect >
&/dev/null
|| setenv path "$:$home/edirect"
./edirect/setup.sh

顯示和提示如下

trying to establish local installations of any missing perl modules (as logged in /users/ucco/edirect/setup-deps.log) .please be patient, as this step may take a little while .entrez direct has been successfully downloaded and installed. in order to complete the configuration process, please execute the following: echo "source ~/.bash_profile" >> $home /.bashrc echo "export path=\$:/users/ucco/edirect" >> $home /.bash_profile or manually edit the path variable assignment in your .bash_profile file. echo "export path=\$path:\$home/edirect" >> $home

/.bash_profile

為了驗證是否安裝完成，終端輸入下面**

echo "***********************"
> installconfirm
echo "esearch version:"
>> installconfirm
esearch -version >> installconfirm
echo "xtract version:"
>> installconfirm
xtract -version >> installconfirm
echo "edirect install status:"
>> installconfirm
esearch -db pubmed -query "babalobi oo[au] and 2008[pdat]"|\
efetch -format xml |
\xtract -pattern author -
if affiliation -contains medicine \
-element initials >> installconfirm
echo "***********************"
>> installconfirm
cat installconfirm
rm installconfirm

如果安裝成功會顯示以下內容

** **** **** **** **** **** *esearch version: 11.6 xtract version: 11.6 edirect install status: ok** **** **** **** **** ****

*

EDirect在linux和mac下的安裝

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Linux 替換 M字元

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