interproscan
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interproscan [2009/09/11 06:27] – 172.26.0.166 | interproscan [2011/07/21 10:27] (current) – aorth | ||
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- | ====== Interproscan ====== | + | ===== Interproscan ===== |
- | Check configuration to use LSF. | + | |
- | Download and install lates databases. | + | Official FTP: ftp://ftp.ebi.ac.uk/ |
- | Change EBI logo to ILRI logo on wait page. | + | ===== Installation ===== |
+ | ==== Requirements ==== | ||
+ | From the readme, in addition | ||
+ | < | ||
+ | 1.1 Perl | ||
+ | The InterProScan package has been developed in Perl5 under UNIX and requires | ||
+ | that various perl modules be installed beforehand. | ||
+ | modules are available via the CPAN website (http:// | ||
+ | * DB_File.pm - the interface to Berkeley DB, which is a part of the standard Perl5 distribution. | ||
+ | * XML:: | ||
+ | BlastProDom and to parse xml outputs. | ||
+ | * XML:: | ||
+ | * English | ||
+ | * File:: | ||
+ | * File:: | ||
+ | * File:: | ||
+ | * File:: | ||
+ | * Sys:: | ||
+ | * Mail:: | ||
+ | * FileHandle | ||
+ | * IO:: | ||
+ | * CGI | ||
+ | * URI:: | ||
+ | * IO:: | ||
+ | |||
+ | Here is a script you can use to test if these modules are working on a particular node: | ||
+ | < | ||
+ | |||
+ | use DB_File; | ||
+ | use XML:: | ||
+ | use XML:: | ||
+ | use English; | ||
+ | use File:: | ||
+ | use File:: | ||
+ | use File:: | ||
+ | use File:: | ||
+ | use Sys:: | ||
+ | use Mail:: | ||
+ | use FileHandle; | ||
+ | use IO:: | ||
+ | use CGI; | ||
+ | use URI:: | ||
+ | use IO:: | ||
+ | use Bio:: | ||
+ | |||
+ | exit;</ | ||
+ | If it is successful you should not see any output. | ||
+ | |||
+ | List all perl modules available in yum: | ||
+ | < | ||
+ | |||
+ | ==== Getting the files ==== | ||
+ | iprscan will unzip into its own folder, so you don't need to create one to hold all these files. | ||
+ | < | ||
+ | wget ftp:// | ||
+ | wget ftp:// | ||
+ | wget ftp:// | ||
+ | wget ftp:// | ||
+ | </ | ||
+ | |||
+ | ==== Unzipping ==== | ||
+ | < | ||
+ | tar zxf iprscan_DATA_33.0.tar.gz | ||
+ | tar zxf iprscan_MATCH_DATA_33.0.tar.gz | ||
+ | tar zxf iprscan_PTHR_DATA_31.0.tar.gz | ||
+ | tar zxf iprscan_v4.8.tar.gz</ | ||
+ | |||
+ | ==== Configuration ==== | ||
+ | Create the destination directory and move the unzipped '' | ||
+ | < | ||
+ | sudo mv iprscan / | ||
+ | cd / | ||
+ | ./ | ||
+ | Wait a sec while it formats the databases... | ||
+ | |||
+ | ==== Testing ==== | ||
+ | < | ||
+ | |||
+ | ==== Apache config ==== | ||
+ | Paste the following in /// | ||
+ | < | ||
+ | Alias /images/ "/ | ||
+ | Alias /tmp/ "/ | ||
+ | |||
+ | | ||
+ | |||
+ | < | ||
+ | | ||
+ | | ||
+ | Order allow, | ||
+ | Allow from all | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | | ||
+ | IndexIgnore */.??* *~ *# */HEADER* */README* */RCS | ||
+ | AllowOverride AuthConfig Limit FileInfo | ||
+ | |||
+ | Order deny, | ||
+ | Deny from all | ||
+ | Allow from .ilri.cgiar.org | ||
+ | </ | ||
+ | And then restart Apache with '' | ||
+ | === Apache write permissions === | ||
+ | Make sure Apache can write to the iprscan folder! | ||
+ | < |
interproscan.1252650456.txt.gz · Last modified: 2010/05/22 14:19 (external edit)