castanyes blaves

Something that I had buried somewhere else

Reading Andreas' manual to install a lightweight DAS server in my

computer:

No root access needed. Just define ALTROOT.

Using GNU Stow:

The approach used by Stow is to install each package into its own

tree, then use symbolic links to make it appear as though the files

are installed in the common tree. Administration can be performed in

the package's private tree in isolation from clutter from other

packages.

Downloading LDAS:

http://www.biodas.org/download/ldas/LDasServer.tar.gz

Problems with permissions:

$# ln -s /usr/local/apache/cgi-bin/das /var/www/cgi-bin/das

DAS servers are of two kinds, reference servers and annotation

servers. We're not setting up a reference DAS server so we won't need

any assembly information. We still need to fetch reference and

annotation data though.

awk 'BEGIN { OFS="\t"; print "[annotations]"; } \

{ \

print "Gene", $10, $3, $2, $1, $4, $5, $7, $6, $8; \

}' human_chr7.gff | tr -d ';' >human_chr7.das

To set the passwords for mysql (for fresh installation):

[avb]$ mysqladmin -u root password "mypassword"

and to define the password for accessing to a specific database:

mysql> USE mydatabase;

mysql> UPDATE user SET Password=PASSWORD("userpassword") WHERE \

User="user_of_mydatabase";

[avb@localhost data]$ mysql --user root -p

Enter password:

Welcome to the MySQL monitor. Commands end with ; or \g.

Your MySQL connection id is 8 to server version: 3.23.58

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> CREATE DATABASE human;

Query OK, 1 row affected (0.00 sec)

mysql> GRANT ALL PRIVILEGES ON human.* TO avb@localhost;

Query OK, 0 rows affected (0.00 sec)

mysql> GRANT FILE ON *.* TO avb@localhost;

Query OK, 0 rows affected (0.00 sec)

mysql> GRANT SELECT ON human.* to avb@localhost;

Query OK, 0 rows affected (0.00 sec)

mysql> QUIT;

Bye

Loading the data:

[avb@localhost scripts]$ ./ldas_load.pl --create --database human ~/ldas/data/human_chr7_ref.das ~/ldas/data/human_chr7.das

Unknown table 'fattribute' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'fgroup' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'fmeta' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'fattribute_to_feature' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'ftype' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'fdna' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

Unknown table 'fdata' at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF/Adaptor/dbi.pm line 1088.

/home/avb/ldas/data/human_chr7_ref.das: loading...

Use of uninitialized value in join or string at /home/avb/ldas/LDasServer-1.11/scripts/Das2GFF.pl line 49, line 3.

Use of uninitialized value in join or string at /home/avb/ldas/LDasServer-1.11/scripts/Das2GFF.pl line 49, line 3.

Argument "" isn't numeric in numeric gt (>) at /home/avb/bioperl/devel/bioperl-live/Bio/DB/GFF.pm line 2221, <> line 1.

/home/avb/ldas/data/human_chr7_ref.das: 1 records loaded

/home/avb/ldas/data/human_chr7.das: loading...

Warning: unable to close filehandle DAS2GFF properly.

/home/avb/ldas/data/human_chr7.das: 784 records loaded

Editing /usr/local/apache/conf/das.conf/human.conf

mapmaster = http://172.22.68.178:8080/cgi-bin/das/human

Changed cgi-bin to allow links to other cgi-bin directories:

AllowOverride None

# Options None

Order allow,deny

Allow from all

Options FollowSymLinks

Adding hardcoded path to Bio/DB/GFF.pm in the

/usr/local/apache/cgi-bin/das script with:

use lib qw(/my/path/to/bioperl-live);

awk 'BEGIN { OFS="\t"; print "[annotations]"; } \

{ \

print "Gene", $10, $3, $2, $1, $4, $5, $7, $6, $8; \

}' human_tm_7.gff | tr -d ';' >human_tm_7.das

To upload the data to the DAS sources, you have to be outside the

EBI/Sanger Firewall, so that your server is visible to the receiving

server, which is in the Sanger Centre.

posted by avilella  # 1:47 PM