Samtools installation

[SeqVicious]

Thank you for your help, it's all working now

[Richard Finney]

type "./samtools" (from cygwin) in the directory you made samools in.

If that does not work, try "./samtools.exe" .

[SeqVicious]

Thank you Richard Finney. I just made these corrections and the make samtools command finished. Unfortunately, when I try to use samtools the samtools command cannot be found. Did something go wrong when I made the executable?

[Richard Finney]

CFLAGS should be on the second line of the make file (Makefile)...

Makefile should be modified like this ...
CFLAGS= -g -Wall -O2 -I/usr/include/ncurses
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log

You'll also need to append the text -Dexpl=exp -Dlogl=log to the DFLAGS line the Makefile in bcftools


ALSO !!!! run "make clean" or remove all the .o (object) files before re-making.

[SeqVicious]

Thanks for trying, Carlos.

I found a fix suggested on another post but I have no idea how to implement it. The fix is adding

CC= gcc
CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
CFLAGS= -I/usr/include/ncurses
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log
KNETFILE_O= knetfile.o

to Makefile. I found three makefiles and none of them had any CFLAGS in the file. Is it even possible to install samtools on windows?

[Carlos Borroto]

Sorry I don't use cygwin so I won't be of much help. Did you try installing libncurses-devel? I see there are several packages in cygwin for it.

[SeqVicious]

I installed anything with the name 'curses' in it during the cygwin installation and I'm still getting the following right before termination.

gcc -c -g -Wall -O2 -D_FILE_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
bam_tview.c:5:20: fatal error: curses.h: No such file or directory
compilation terminated
makefile:21: recipe for target 'bam_tview.o' failed
make:** [bam_tview.o] Error 1

I can't find curses.h to install in cygwin. I don't know what else to do from here.

[SeqVicious]

I'm on windows 7 and I'm using cygwin. I just installed zlib by updating cygwin and the command got much further. This time curses.h failed and the command was terminated. I'll try installing curses.h to see if that works.

[Carlos Borroto]

gbzf.h:29:28: fatal error: zlib.h: No such file or directory

Hi, you don't have zlib in your system. Could you tell me in what operating system are you installing Samtools?

[SeqVicious]

Hi all,

I'm very new to bioinformatics and all I'm trying to do is index a bam file so I can view the pileup in IGV. I've downloaded the latest version of samtools unpacked it successfully. I'm now trying to install it but I'm running into an error after the 'make samtools' command. Make clean works just fine but the following error occurs after 'make samtools'.

$ make samtools
make[1]: Entering directory <path>
gcc -c -g -Wall -O2 -D_FILE_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.o
In file included from bgzf.c:36:0:
gbzf.h:29:28: fatal error: zlib.h: No such file or directory
compilation terminated
Makefile:21: recipe for target 'bgzf.o' failed
make[1]: *** [bgzf.o] Error 1
make[1]: Leaving directory <path>
$CC= gcc
gcc: no input filesr] Error 1

It looks like it's having trouble with one of the files. Since I only need to be using a few of the samtools options can I just delete the files that give problems? I've also tried redownloading samtools a couple of times and the same error shows up.