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

[Keith Jolley]

Your confusion stems from the fact that /usr/local/bioinf and /usr/software
are equivalent.

If you 'ls -l' from /usr you'll see that software is a symlink to
local/bioinf, so you could use either.

Keith

> -----Original Message-----
> From: bio-linux-bounces at envgen.nox.ac.uk [mailto:bio-linux-
> bounces at envgen.nox.ac.uk] On Behalf Of Jose A. Andres
> Sent: 05 May 2006 16:03
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] phred/phrap/consed installation on Bio-linux
> 
> 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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