Mirror

Obtain the latest version of mirror from ftp://sunsite.org.uk/packages/mirror/mirror.tar.gz"

Create a subdirectory for mirror, cd into it and unpack the tar file:

mkdir /opt/mirror
cd /opt/mirror
tar -zxvf ..../mirror.tar.gz

perl install.pl

User perl from: /usr/bin/perl
Store commands in: /usr/local/bin
Support libraries in: /usr/local/lib/mirror

Ensure that /usr/local/lib/mirror is in the PERLLIB path. Edit /etc/profile and add the line:

export PERLLIB="/usr/local/lib/mirror"

Alter the following in mirror.defaults

    package=defaults
        # The LOCAL hostname - if not the same as `hostname`
        # (I advertise the name sunsite.org.uk but the machine is
        #  really swallow.sunsite.org.uk.)
        hostname=sapc77.rdg.ac.uk
        # Keep all local_dirs relative to here
        local_dir=/data/
        # The local_dir must exist FIRST
        #local_dir_check=true
        remote_password=a.c.r.martin@reading.ac.uk
        #
        # For Reading, we need to go via the FTP proxy server
        #
        proxy=true
        proxy_gateway=ftpproxy.rdg.ac.uk
        proxy_ftp_port=21

and place that file in /usr/local/lib/mirror

Create a subdirectory for the mirror packages:

mkdir /usr/local/lib/mirror/packages

and create the mirroring packages (each in a separate file with the package name):

File: enzyme

package=enzyme
        comment=enzyme database from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/enzyme/
        local_dir=/data/enzyme/
        mail_to=sequence_users

File: genbank

package=genbank
        comment=genbank database from NCBI - exclude ESTs, GSSs, HTSs
        site=ftp.ncbi.nlm.nih.gov
        remote_dir=genbank/
        local_dir=/data/genbank/
        exclude_patt=(^|/)(gbest|gbgss|gnhtg)
        mail_to=sequence_users

File: imgt

package=imgt
        comment=imgt database from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/imgt/
        local_dir=/data/imgt/
        mail_to=immunology_users

File: kabat

package=kabat
        comment=Kabat database from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/kabat/fixlen/
        local_dir=/data/kabat/
        do_deletes=false
        mail_to=immunology_users

File: p53

package=p53
        comment=p53 database from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/p53/
        local_dir=/data/p53/
        do_deletes=false
        mail_to=p53_users

File: pdb

package=pdb
        comment=PDB from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/pdb/pub/pdb_data/all_entries/uncompressed_files/
        local_dir=/data/pdb/
        mail_to=pdb_users

package=pdb-obsolete
        comment=PDB obsolete entries from EBI
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/pdb/pub/pdb_data/obsolete_entries/
        local_dir=/data/pdb_obsolete/
        mail_to=pdb_users

File: redhat

package=redhat
        comment=Redhat from sunsite mirror
        site=sunsite.org.uk
        remote_dir=Mirrors/ftp.redhat.com/redhat/redhat-6.0/i386/
        local_dir=/data/redhat/redhat-6.0/i386/

File: package=pdate

package=redhat_update
        comment=Redhat updates from sunsite mirror
        site=sunsite.org.uk
        remote_dir=Mirrors/ftp.redhat.com/redhat/updates/6.0/
        local_dir=/data/redhat/updates/6.0/
        exclude_patt=(^|)(alpha)

File: swissprot

package=swissprot
        comment=SwissProt from EBI: top level files
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/swissprot/
        local_dir=/data/swissprot/
        recursive=false
        do_deletes=false

package=swissprot-release
        comment=SwissProt from EBI: actual release
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/swissprot/release/
        local_dir=/data/swissprot/release/
        mail_to=sequence_users

package=swissprot-updates
        comment=SwissProt from EBI: updates
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/swissprot/updates/
        local_dir=/data/swissprot/updates/
        mail_to=sequence_users

package=swissprot-old
        comment=SwissProt from EBI: old versions
        site=ftp.ebi.ac.uk
        remote_dir=pub/databases/swissprot/sw_old_releases/
        local_dir=/data/swissprot/sw_old_releases/

Create mail aliases in /etc/aliases (ammend as required):

        sequence_users: andrew
        pdb_users:      andrew, E.G.Hutchinson@reading.ac.uk
        p53_users:      andrew
        immunology_users: andrew

and run

newaliases

to update the sendmail alias database.

Create a cron job to run the mirror jobs. Create the file /etc/cron.daily/mirror.cron:

#!/bin/bash
for pkg in /usr/local/lib/mirror/packages/*
do
   mirror $pkg
done

and make it executable:

chmod +x /etc/cron.daily/mirror.cron