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how to install Pfam_scan.pl under linux (ubuntu)  

2014-09-09 04:19:05|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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This may seem silly for the pros but I indeed tried several times before make successful installation of pfam_scan.pl on my ubuntu. And I believe this blog is definitely more useful than the installation manual on Pfam FTP for beginners.
Steps:
download the binary file from Pfam FTP from here: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/
download the required database from Pfam FTP from here: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release( As I only use PfamA so I just download...)
download HMMER3 from here: http://hmmer.janelia.org/software
insall perl and bioperl
use command: 
sudo apt-get install perl ( replace perl with bioperl for installation of bioperl) 

the system will ask for password just type it in and you will see its installing

5.    install Moose
you need to change to root in order to install Moose from CPAN so you first do this :

sudo -i ( the system will ask for password type it in and youll find the user name change to root marked in red. its ready to go now) 
then use CPAN to install Moose use this:

CPAN Moose ( this will take a while)

6. install HMMER3

cd /home/shuixia100/Desktop/hmmer3
and start installation use the default parameters ( i dont know much about the advanced option usage by now)

./configure
make 
make check
make install

it just works well (dont ask what if it dont work well i dont know either) and by default the file in  installed in /usr/local/bin. now you need to add the hmmer into your path by:
export PATH=/usr/local/bin/:$PATh

check if you have make it works by  run hmmer outside the folder of hmmer by:
hmmscan -h
 
7.   install pfam_scan.pl by adding pfam_scan.pl to your perl path by:
export PERL5LIB=/path/to/pfam_scanDir:$PATH

check if it is insatlled by this:
perl -V
the path to your pfam_scan.pl should be listed if it is successfully added

8.   index the pfamA database by hmmerspress like this:
change directory to where you put your Pfam-A.hmm and run
hmmpress Pfam-A.hmm

9.  Congradulation You are Ready to go now! just leave a example syntax of using pfam_scan.pl here:
cd /home/shuixia100/Desktop/Pfam_scan./pfam_scan.pl -fasta ./ST07-7-aa-contigs-100aacutaa -dir ./ -e_seq 1e-4 -e_dom 1e-4 -clan_overlap -outfile ST07-7-aa-contigs-100aacutaa.output

For the detailed usage refer to the manual in the downloaded file.
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