This page was last updated on Saturday, 10-Nov-2018 15:18:43 CST
Installation notes for PAGIT version 1 - Feb 14, 2012
Home Page
Prerequisites
"We assume that java and the tcsh-shell is installed"
Java instructions
$ sudo apt-get install tcsh
PAGIT relies on other freely available bioinformatics software developed by third parties. The list of this third-party software is as follows:
- Artemis - annotation & BAM visualization tool
- ACT - a DNA sequence comparison viewer
- BLASTALL - sequence comparison tool
- BWA - read mapping tool (Burrows-Wheeler transformation based)
- MUMmer - sequence comparison tools
- SAMTOOLS - suite to work with BAM files
- SMALT - read mapping tool (k-mer based)
- VELVET - short read assembler
Installation
Note, separate instructions for installing RATT
- $ cd /programinstallers/
- $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/PAGIT.V1.64bit.tgz
- $ cd /usr/local/bin
- $ tar -zxvf /programinstallers/PAGIT.V1.64bit.tgz
- $ ./installme.sh
Installation successfully!
If you intend to use RATT to transfer annotation for species with different start / codons or splice sites, please adapt the file /usr/local/bin/PAGIT/RATT/RATT.config.
Each time you run please type: source /usr/local/bin/PAGIT/sourceme.pagit
Alternatively include the line in your ~/.bashrc file.
We assume that java and the tcsh-shell is installed
- $ rm installme.sh
- To allow scripts to find Perl, did this
$ ln -s /usr/bin/perl /usr/local/bin/perl
- Under "Bugs" saw this text: The script to join chromosomes for ABACAS was missing. Please
download it
and unzip the content in the PAGIT/ABACAS directory.
$ cd /usr/local/bin/PAGIT/ABACAS/
- $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/PAGIT_MissingScripts.zip
- $ unzip PAGIT_MissingScripts.zip
Archive: PAGIT_MissingScripts.zip
replace joinMultifasta.pl? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
inflating: joinMultifasta.pl
replace split2Multifasta.pl? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
inflating: split2Multifasta.pl
inflating: SeperateSequences.pl
inflating: splitABACASunion.pl
- $ rm PAGIT_MissingScripts.zip
- Make an alias to the setup script
$ sudo nano /etc/profile
…
alias pagitinit='source /usr/local/bin/PAGIT/sourceme.pagit'
…