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

[Jose A. Andres]

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!!!!!!!!!!!!!!!!!!