User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/01/30

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pftools installation on Ubuntu 10.10

I imagine anyone running into this would know what to do, but I had to do some googling to figure it out, so I thought it worthy of inclusion. pSORTb lists pftools as a dependency, but attempted installation fails because the g77 Fortran compiler is deprecated in Ubuntu since 8.04.

Compiling with


	tar -xzvf pftools_23.tar.gz
	make all


returns an error:

	james@augustus:~/Data/bdcost/programs/pftools$ make all
	gcc -c io.c -o io.o 
	g77 -O2 -init-local-zero -fno-automatic io.o gtop.f -o gtop 
	make: g77: Command not found
	make: *** [gtop] Error 127


In order to fix it one needs to correct the Makefile from

# M A K E F I L E   F O R   P F T O O L S  R E L E A S E  2.3
# $Id: Makefile,v 2.16 2003/11/28 11:54:37 vflegel Exp $

PROGS = gtop pfmake pfscan pfw ptoh htop \
        pfscale pfsearch psa2msa 2ft 6ft ptof
MANS =  gtop.1 pfmake.1 pfscan.1 pfw.1 ptoh.1 htop.1 pfscale.1 \
        pfsearch.1 psa2msa.1 2ft.1 6ft.1 ptof.1 psa.5 xpsa.5

F77   = g77
CC    = gcc
FFLAGS= -O2 -init-local-zero -fno-automatic io.o
#PRFLAG= -g -pg


F77   = gfortran
CC    = gcc
FFLAGS= -O2 -init-local-zero -fno-automatic io.o -std=legacy

This allows gtop to compile, but pfmake errors out with:

james@augustus:~/Data/bdcost/programs/pftools$ make all
gfortran -O2 -std=gnu -finit-local-zero -fno-automatic io.o  pfmake.f -o pfmake  
/tmp/ccWx73Ga.o: In function `MAIN__':
pfmake.f:(.text+0x12665): undefined reference to `fdate_'
collect2: ld returned 1 exit status
make: *** [pfmake] Error 1

Now I see that there are precompiled executables on the site. Facepalm. Try again tomorrow.

Glimmer3 results for Bdellovibrio strain W

Ran with default settings against the raw contigs. Attached at User:James_Estevez/Notebook/Spring_2011:_Bdellovibrio_Independent_Study/2011/01/30/Bdellovibrio_strain_W_glimmer3.predict and User:James_Estevez/Notebook/Spring_2011:_Bdellovibrio_Independent_Study/2011/01/30/Bdellovibrio_strain_W_glimmer3.detail