update PlasMapper installation, with a patch, according to Stephane comments on issue #3

doc/install_plasmapper.md

@@ -5,6 +5,10 @@ On the targeted server type the following commands in a terminal :
    cd opts/
    tar xfvz PlasMapper_download.tar.gz
    cd PlasMapper
+
+   # fix a bug due to spaces and \ in batik.jar
+   mv ../PlasMapper_patch_batik.jar ./WebContent/WEB-INF/lib/batik.jar
+
    # modify installdir as /var/lib/tomcat9
    sed -i 's/\/home\/tomcat/\/var\/lib\/tomcat9/g' build.xml
    # modify servletjar as /usr/share/tomcat9/lib/servlet-api.jar
@@ -19,12 +23,9 @@ On the targeted server type the following commands in a terminal :
    ant build
    sudo ant install
    
-   sudo rm -Rf /var/lib/tomcat9/webapps/PlasMapper/tmp
-   sudo ln -s /tmp/tomcat9-tomcat9-tmp/ /var/lib/tomcat9/webapps/PlasMapper/tmp
    echo '<?xml version="1.0" encoding="UTF-8"?><Context path="/myapp" allowLinking="true"></Context>' > context.xml
    sudo mv context.xml /var/lib/tomcat9/webapps/PlasMapper/META-INF/
    sudo systemctl restart tomcat9
-   # After these steps, PlasMapper works on your server at the url http://localhost:8080/PlasMapper
      
    sudo chown root:www-data /var/lib/tomcat9/webapps/PlasMapper/dataBase/db_vectorFeature/*.*
    sudo chmod 664 /var/lib/tomcat9/webapps/PlasMapper/dataBase/db_vectorFeature/*.*
@@ -36,10 +37,8 @@ On the targeted server type the following commands in a terminal :
    sudo chown -R tomcat:tomcat /var/lib/tomcat9/webapps/PlasMapper/
    sudo service tomcat9 restart
    
-   #  Now, plasmid features are ready to be searched by MyLabStocks via BLAST queries.
-   cd ../../..
 ```  
-Now you should have a plasMapper instance available here:
+Now you should have a PlasMapper instance available here:
 http://localhost:8080/PlasMapper