[Bio-Linux] phred/phrap/consed installation on Bio-linux

[Bela Tiwari]

Hi Jose,

It sounds like you already have licenses for phred and phrap. If so, we can provide you with Bio-Linux packages for them, which will be much easier to install. Can you please write to the helpdesk address: helpdesk at envgen.nox.ac.uk to confirm that you have licenses and then we can help you from there.

We haven't packaged consed for Bio-Linux yet, so at the moment there is not much we can say except that if you follow the instructions given by the authors, it is possible to get it running on Bio-Linux. I am planning on making a package for consed, but I probably won't have time for this until June at the earliest. I  know that others in the community have managed to install Consed on Bio-Linux successfully, but their feedback was that it wasn't a fun task.

If you write to the helpdesk about phred and phrap, please let us know (in general terms) what you are trying to do with these tools so that we can let you know of any other programs on Bio-Linux that might be of help to you.

cheers

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> jaa53 at cornell.edu 05/05/2006 16:03 >>>
Hi all,

 (Thanks in advance for all your help)

I'd like  to install phred/phrap/consed into bio-linux4 but since I am not
funded by the NEBC, I have to do it from the original files I got from
Phil's Green lab. I should be able  to do it, but I am a bit confuse with
the symlinks (and another couple of things) and  I'd like to get some
extra advice from the community (if possible).

I realise how busy we all are and I'd really appreciate any suggestions
and comments.THANKS!!

Cheers,

/Jose

Here is what I am planning:

# reading from a flash-drive...

mount /media/usbkey

# storing source code  on /usr/local/src

sudo mkdir -p /usr/local/src/phred

#moving stuff around...

sudo mv /media/usbkey/ /usr/local/src/phred

#uncompressing the file ...

uncompress phred-dist-020425.c-acd.tar.Z
tar xvf phred-dist-020425.c-acd.tar

# I've read somewhere (do not remember exactly where) that to compile
phred with the correct optimization I need to edit one line of the make
file
 (Soooo....

nano Makefile ("remove # from the LXFLAGS = -DX86_GCC_LINUX line and save).

#then...

./make

#now I need to copy the executable of this version (to keep the bio-linux
standards) into the right place. I am assuming

/usr/software/phred/phred_020425). Am I right?  or shall I put it into
/usr/local/bioinf?? Sooo I create the new dir


sudo mkdir -p /usr/software/phred/phred_020425 (or

# and copy the executable there

sudo cp phred /usr/software/phred/phred_020425

# As I said I am a bit confuse cause both /usr/software and
/usr/local/bioinf seem to have the same stuff in...

!!!!!! Do I have to also copy the make the dir 
/usr/local/bioinf/phred/phred_02004425 and cp the Phred executable there?

!!!!!! do I have to make a symlink? if so, shall I make it in the same
place? That is

sudo ln -s /usr/software/phred/phred_020425 /usr/software/phred/phred

!!!!!!! or in the /usr/local/bioinf/ or both?

sudo ln -s /usr/software/phred/phred_020425 /usr/local/bioinf/phred

# Any suggestions?

# I shall move the phred parameter file to the right location.Something
like this?

sudo cp phredpar.dat /usr/local/bioinf/phred/phred/prhredpar.dat

#set the enviroment..

nano -w /usr/local/bioinf/config_files/bioenvrc

(Add and save..)

export PHRED_PARAMETER_FILE=/usr/local/bioinf/phred/phred/phredpar.dat;
export PATH=$PATH:/usr/local/bioinf/blast/blast:
/usr/local/bioinf/netblast/netblast: /usr/local/bioinf/phred/phred:
/usr/local/bioinf/phrap/phrap:/usr/sbin

#installing

WOULD THIS WORK??? IF so I shall also be able to install phrap and consed
in a very similar way...

THANKS EVERYONE!!!!!!!!!!!!!!!!!!




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