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Old 06-26-2013, 01:25 PM   #1
jwag
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Location: USA

Join Date: Apr 2013
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Default PAGIT installation

Has anyone successfully installed PAGIT on a linux server yet (http://www.sanger.ac.uk/resources/software/pagit/)? I've followed the instructions but I can't get it to work:

Code:
user:/my/dir/:505 > tar xzf PAGIT.V1.64bit.tgz 

user:/my/dir/:504 > bash ./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 /disk/scratch/jpod/A_limnaeus/tools/PAGIT/RATT/RATT.config.

Each time you run please type: source /disk/scratch/jpod/A_limnaeus/tools/PAGIT/sourceme.pagit
Alternatively include the line in your ~/.bashrc file.

We assume that java and the tcsh-shell is installed

user:/my/dir/:524 > source PAGIT/sourceme.pagit 
path=/disk/scratch/jpod/A_limnaeus/tools/PAGIT: Command not found.
PAGIT_HOME=/vol/apps/user/bin/: Command not found.
PATH=/vol/apps/user/bin/: Command not found.
PILEUP_HOME=/vol/apps/user/bin/: Command not found.
ICORN_HOME=/vol/apps/user/bin/: Command not found.
SNPOMATIC_HOME=/vol/apps/user/bin/: Command not found.
RATT_HOME=/vol/apps/user/bin/: Command not found.
RATT_HOME: Undefined variable.
Any help would be appreciated. I'm trying to get RATT running.
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Old 07-12-2013, 05:22 AM   #2
ThomasDOtto
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Location: Cambrdige, UK

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Hi,

which shell are you using? PAGIT works best with the bash shell. Just type
bash
and then repeat the source command.

Cheers,
Thomas
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Old 07-29-2013, 12:56 AM   #3
sivasubramani
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Dear All,

I was trying to use PAGIT - Post Assembly Genome Improvement Toolkit, for one of my assembly. I could not find any proper manual to explaing the steps. when I opened the dotestrun.sh script I could see there are some mandatory input files needed to run the suit. FastQ files, reference fasta file and query fasta file are someof those. Along with these we need to provide reference embl(*.embl) file. I did not understand what that file and from where I can get that file.

Thanks,

Siva
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Old 07-29-2013, 02:32 AM   #4
ThomasDOtto
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Default nature protocol

Hi Siva,

well, there is a nature protocol paper that explains each step:

http://www.nature.com/nprot/journal/....2012.068.html
or
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648784/

I will make it more obvious on the web page... I hope this helps. If you have any, please let us know. There are also some bug fixes:
http://www.sanger.ac.uk/resources/software/pagit/#Bugs

Cheers,
Thomas

PS: We are planing to update icorn2, to correct pacbio assemblies soon... so a pagit update should come soon...
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Old 07-29-2013, 04:08 AM   #5
ThomasDOtto
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I just checked the pagit webpage, and indeed it was not very clear. It should be better now
http://www.sanger.ac.uk/resources/software/pagit/

Thanks,
Thomas
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Old 07-29-2013, 08:47 AM   #6
jwag
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Hi, just an update. I got PAGIT installed and partially running, but the problem was that my GLIBCXX was outdated, so I can't use it until it gets updated on my server. Thanks for updating the instructions, Thomas.
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