SAM tools on a mac

[qnc]

Hi,

I have tried to down load and instal SAMTools on my mac to make VCF files from a BAM file I have but it is not working?

What I did:
I tried to follow these instructions here (http://sourceforge.net/apps/mediawik...stall_software)

1) went here and waited for auto download (http://sourceforge.net/projects/bio-...r.bz2/download) as I didn't have "wget" installed

2) Moved it to a convent location

3) Open up terminal (Version 2.2.2 (303))

4) tar -jxf samtools-0.1.18.tar.bz2

5) cd samtools-0.1.18

6) ls gives
UTHORS bam2bcf.c bam_index.c bam_sort.c cut_target.c klist.h misc sam_view.c
COPYING bam2bcf.h bam_lpileup.c bam_stat.c errmod.c knetfile.c phase.c sample.c
ChangeLog bam2bcf_indel.c bam_mate.c bam_tview.c errmod.h knetfile.h razf.c sample.h
INSTALL bam2depth.c bam_md.c bamtk.c examples kprobaln.c razf.h samtools.1
Makefile bam_aux.c bam_pileup.c bcftools faidx.c kprobaln.h razip.c win32
Makefile.mingw bam_cat.c bam_plcmd.c bedidx.c faidx.h kseq.h sam.c
NEWS bam_color.c bam_reheader.c bgzf.c kaln.c ksort.h sam.h
bam.c bam_endian.h bam_rmdup.c bgzf.h kaln.h kstring.c sam_header.c
bam.h bam_import.c bam_rmdupse.c bgzip.c khash.h kstring.h sam_header.h

7) Tried Make but got -bash: make: command not found

8) I installed make when I downloaded xtools to get BEDTools-v2.13.3 working.

9) BEDTools in now not working either!!

Do I have to download the xtools all over again?

[dpryan]

Either you don't have the developer tools installed correctly or where ever "make" is isn't in your PATH.

[qnc]

I upgraded to OSX Lion do you think that could cause it.

How do I set a path to see if the make works again or where is the make directory likely to be so that I can test it in that folder to see if there is a problem with the program itself?

[chadn737]

Yes. I had the same problem when I upgraded to Lion. You need to reinstall X tools.

[maubp]

On Lion you can get Xcode from the Mac App Store (free, but a big download). That will install gcc, make, etc.

[Phantom123]

i had encountered a similar problem. you need to install Xcode properly.

[qnc]

Awesome downloading now.

[qnc]

Got this error message during install will it cause problems?

The system extension “/System/Library/Extensions/hpPlugInInit.kext” was installed improperly and cannot be used. Please try reinstalling it, or contact the product’s vendor for an update.

[dpryan]

hpPlugInInit.kext is some sort of printer driver from HP, so it seems unlikely to cause any problems with anything no printing related (assuming it didn't crash the installation of the developer tools).

[qnc]

Ace!

in the bwa folder it has:
COPYING bwa.1 bwt.h bwtgap.c bwtsw2_aux.c khash.h main.c stdaln.h
ChangeLog bwa.txt bwt_gen bwtgap.h bwtsw2_chain.c kseq.h main.h utils.c
Makefile bwape.c bwt_lite.c bwtindex.c bwtsw2_core.c ksort.h qualfa2fq.pl utils.h
NEWS bwase.c bwt_lite.h bwtio.c bwtsw2_main.c kstring.c simple_dp.c
bntseq.c bwaseqio.c bwtaln.c bwtmisc.c cs2nt.c kstring.h solid2fastq.pl
bntseq.h bwt.c bwtaln.h bwtsw2.h is.c kvec.h stdaln.c

but when in that folder and I type "make" I get:

-bash: make: command not found

Do I have to set the path or something?

Xcode finished installing and start up ok.

[dpryan]

Possibly, type the following (without the quotes): "echo $PATH" and then paste what you get as output. I don't have my laptop handy as I'm in lab at the moment but I recall that the developer tools are installed under /Developer/usr/bin or something like that. Also, make sure you have the "command line tools" part of Xcode installed since that'll probably be what contains make and the other useful utilities.

[qnc]

I get

prompt> echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

also in /Developer/usr/bin
prompt> ls -F
BuildStrings* dsymutil* mdcheckschema*
CpMac* dwarfdump* merge*
DeRez* dyldinfo* mig*
DevToolsSecurity* filesynctool* mkdep*
GetFileInfo* flex* mksdk*
ImageUnitAnalyzer* flex++@ momc*
MergePef* g++@ mpic++@
MvMac* g++-4.0* mpicc@
PPCExplain* g++-4.2* mpicxx@
ResMerger* gatherheaderdoc* mpif77@
Rez* gcc@ mpif90@
RezDet* gcc-4.0* nasm*
RezWack* gcc-4.2* ndisasm*
SetFile* gcov@ nm*
SplitForks* gcov-4.0* nmedit*
UnRezWack* gcov-4.2* opal_wrapper*
WSMakeStubs* gdb* opendiff*
aclocal* glibtool* otool*
aclocal-1.10* glibtoolize* packagemaker@
agvtool* gm4* pagestuff*
amlint* gnumake* powerpc-apple-darwin10-cpp-4.2.1*
ar* gperf* powerpc-apple-darwin10-g++-4.0.1*
as* gprof* powerpc-apple-darwin10-g++-4.2.1*
asa* hdxml2manxml* powerpc-apple-darwin10-gcc-4.0.1*
atos* headerdoc2html* powerpc-apple-darwin10-gcc-4.2.1*
autoconf* heap* powerpc-apple-darwin10-llvm-g++-4.2@
autoheader* heapdiff.pl* powerpc-apple-darwin10-llvm-gcc-4.2@
autom4te* i686-apple-darwin10-cpp-4.2.1* projectInfo*
automake* i686-apple-darwin10-g++-4.0.1* pump*
automake-1.10* i686-apple-darwin10-g++-4.2.1* ranlib@
autoreconf* i686-apple-darwin10-gcc-4.0.1* rb_nibtool@
autoscan* i686-apple-darwin10-gcc-4.2.1* rcs*
autoupdate* i686-apple-darwin10-llvm-g++-4.2@ rcs2log@
bison* i686-apple-darwin10-llvm-gcc-4.2@ rcsclean*
bsdmake* ibtool* rcsdiff*
c++@ ident* rcsmerge*
c++-4.0* ifnames* rebase*
c++-4.2* indent* redo_prebinding*
c89* install_name_tool* rlog*
c99* instruments* rpcgen*
cc@ javaconfig* sdef*
ci* javatool* sdp*
clang* ld* segedit*
cmpdylib* ld_classic* size*
co* leaks* strip*
compileHelp* lex* svk*
config* libtool* unifdef*
cpp* llvm-cpp-4.2@ unifdefall*
cpp-4.0* llvm-g++@ unwinddump*
cpp-4.2* llvm-g++-4.2@ vers_string*
ctags* llvm-gcc@ vgrind*
ctf_insert* llvm-gcc-4.2@ what*
cvs* lorder* xcodebuild*
cvsbug* lsdistcc* xcodeindex*
desdp* m4* xed*
distcc* make@ xml2man*
distccmon-text* malloc_history* yacc*
docsetutil* mapc*


"make" is an alias of "gnumake"

Is that correct?

[dpryan]

Sounds right, just add that to your path (remove quotes, I'm assuming that you're using bash): "export PATH=$PATH:/Developer/usr/bin" and then typing make should work. To make the path change permanent you can edit the ".bashrc" file in your home directory.

[qnc]

Cool it works but not quite!!!

LOL

prompt>export PATH=$PATH:/Developer/usr/bin
prompt>make
make: *** No targets specified and no makefile found. Stop.

How do I edit the .bashrc file can I just do a "cat" or something as I don't trust my text edit to do the job properly.

What would people recommend for editing files with the correct line breaks and CR etc..

[dpryan]

When you issue the "make" command you need to be in the directory containing the samtools source code ("make" looks for a file called "Makefile" in the current directory).

You can add this path to your .bashrc file with the following (you need to include the quotes):

echo "export PATH=\$PATH:/Developer/usr/bin" >> ~/.bashrc