samtools installation

[nicedad]

Hi everyone,
Can anyone show me how to install samtools step by step?
I hope someone answers this naive question::

best,

[nilshomer]

What operating system? Are you a user or administrator?

[nicedad]

Hi nilshomer,
am using linux suse on 64 bus machine. I've got Win. 7 on the same machine also.
I am the admin.

cheers,

[nilshomer]

you download the source, compile, then move the binary to your local bin directory. Here are some links to help (the first few links from google):

http://open.helicosbio.com/helisphere_user_guide/ch02.html

http://seqanswers.com/forums/showthread.php?t=7391

http://ged.msu.edu/angus/tutorials-2011/snp_tutorial.html

http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX

[nicedad]

Thanks milshmore, unfortunately still have the following error.
When I use the quick and dirty SAMtools install, i get this:

[COLOR="Red"]vo-zapus:/windows/D/samtools # make
make[1]: Entering directory `/windows/D/samtools'
make[2]: Entering directory `/windows/D/samtools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/windows/D/samtools'
make[2]: Entering directory `/windows/D/samtools/bcftools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/windows/D/samtools/bcftools'
make[2]: Entering directory `/windows/D/samtools/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/windows/D/samtools/misc'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
make[1]: gcc: Command not found
make[1]: *** [bam_tview.o] Error 127
make[1]: Leaving directory `/windows/D/samtools'
make: *** [all-recur] Error 1[/COLOR]

And when I use pysqlite method I get this:

[COLOR="Red"]evo-zapus:/windows/D/pysqlite # python setup.py build
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pysqlite2
copying lib/dbapi2.py -> build/lib.linux-x86_64-2.7/pysqlite2
copying lib/dump.py -> build/lib.linux-x86_64-2.7/pysqlite2
copying lib/__init__.py -> build/lib.linux-x86_64-2.7/pysqlite2
creating build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/dbapi.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/dump.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/factory.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/hooks.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/py25tests.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/regression.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/transactions.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/types.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/userfunctions.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
copying lib/test/__init__.py -> build/lib.linux-x86_64-2.7/pysqlite2/test
running build_ext
building 'pysqlite2._sqlite' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -DMODULE_NAME="pysqlite2.dbapi2" -DSQLITE_OMIT_LOAD_EXTENSION=1 -I/usr/include/python2.7 -c src/module.c -o build/temp.linux-x86_64-2.7/src/module.o
unable to execute gcc: No such file or directory
error: command 'gcc' failed with exit status 1[/COLOR]

could anyone help please what a library am missing (gcc)?

[nicedad]

Additionally, I tried to install it using cygwin unfortunately got this message:

akram@evo-zapus /cygdrive/c/samtools-0.1.9
$ make
make[1]: Entering directory `/cygdrive/c/samtools-0.1.9'
make[2]: Entering directory `/cygdrive/c/samtools-0.1.9'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9'
make[2]: Entering directory `/cygdrive/c/samtools-0.1.9/bcftools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9/bcftools'
make[2]: Entering directory `/cygdrive/c/samtools-0.1.9/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9/misc'
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_tview.c -o bam_tview.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sam_view.c -o sam_view.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_mate.c -o bam_mate.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_stat.c -o bam_stat.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_color.c -o bam_color.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bamtk.c -o bamtk.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. kaln.c -o kaln.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam2bcf.c -o bam2bcf.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. errmod.c -o errmod.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sample.c -o sample.o
gcc -I/usr/include/ncurses -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o   bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o     bamtk.o kaln.o bam2bcf.o errmod.o sample.o libbam.a -lm  -lcurses  -lz -Lbcftools -lbcf
make[1]: Leaving directory `/cygdrive/c/samtools-0.1.9'
make[1]: Entering directory `/cygdrive/c/samtools-0.1.9/bcftools'
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I.. -I. call1.c -o call1.o
gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I.. -I. main.c -o main.o
gcc -I/usr/include/ncurses -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm  -lz -L. -lbcf
./libbcf.a(prob1.o): In function `mc_cal_y':
/cygdrive/c/samtools-0.1.9/bcftools/prob1.c:275: undefined reference to `_expl'
collect2: ld returned 1 exit status
Makefile:34: recipe for target `bcftools' failed
make[1]: *** [bcftools] Error 1
make[1]: Leaving directory `/cygdrive/c/samtools-0.1.9/bcftools'
Makefile:26: recipe for target `all-recur' failed
make: *** [all-recur] Error 1

[Ivan Castro]

I got the same problem. This still without some solution?

[sklages]

What is "same problem"? With cygwin, suse,..? Errors?