CNVnator Install Instructions

[dmacmillan]

Hello all, I managed to install CNVnator after much hair-ripping. But now that I have figured everything out, follow the steps to this procedure and hopefully you will have no more issues with installation! Here we go:

1. Install "root" http://root.cern.ch/drupal/content/downloading-root

2. Once you have downloaded the package, unzip it, personally I use this code to untar things...

tar -zxvf [name of tar file]

where you replace [name of tar file] with the actual name of your tar file e.g. "root_v5.32.00.source.tar.gz" (without quotations)

3. now you have a folder called "root" containing everything inside the package you just extracted. Note the path to this "root" folder and save that path somewhere. I will refer to the "root" folder path as "rootpath" from now on

4. Now you want to open up a terminal window and type the commands to install root, which is fairly simple.

cd root

./configure

wait for it to finish....

make

wait again....
done!

5. NOW you want to download CNVnator http://sv.gersteinlab.org/cnvnator/

6. To unzip it you can do it conventionally or use terminal

unzip -o [zip file name]

7. You now have a folder called "CNVnator" or whatever you extracted it to. So just do the following commands from terminal:

cd CNVnator

now if you type "ls" and hi enter you should see the src, license, and readme

cd src/samtools

make

now wait for it to finish...

cd ..

now your back in the "src" directory

EVERYTHING up until this point should just work. BUT the next code you type will not unless you do the following first, so just follow...

export ROOTSYS=[rootpath]

*recall that "rootpath" is the file path to your ".../root" folder where root is installed
Now type

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib

and hit enter. No errors should come up.

8. Now for the final step... cd back into your CNVnator/src folder and type "make" and hit enter. You should get no errors and now will be able to use CNVnator! Happy analyzing!

[aaronh]

What platform are you using? I'm having a real hard time getting it to compile on OSX 10.7 with root 5.32.

[dmacmillan]

CentOS 2.16.0, fairly old, but still capable. What part exactly are you stuck on?

[aaronh]

I can get root to compile and the ROOTSYS and LD_LIBRARY_PATH are pointing to the right places. The problem (I think) is getting CNVator to link to libbam.a. I'v tried the included samtools and also the latest version but each time I get an error like this:

g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c HisMaker.cpp -o obj/HisMaker.o
g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c AliParser.cpp -o obj/AliParser.o
g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c Genotyper.cpp -o obj/Genotyper.o
g++ -pthread -m64 -I/Users/aaron/bin/root/include -Isamtools -c Genome.cpp -o obj/Genome.o
g++ -pthread -m64 -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Genome.o samtools/libbam.a -L/Users/aaron/bin/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -pthread -lm -ldl
Undefined symbols for architecture x86_64:
"_deflateInit2_", referenced from:
_deflate_block in libbam.a(bgzf.o)
....
"_deflateSetHeader", referenced from:
_razf_open_w in libbam.a(razf.o)
ld: symbol(s) not found for architecture x86_64

Any ideas?

[dmacmillan]

Can you type "set" without quotations into your command line and paste the results of ROOTSYS and LD_LIBRARY_PATH? I had a similar error and it turned out my LD_LIBRARY_PATH was not set correctly, each time you open a new terminal it will reset so you must do it all in one go to compile CNVnator.

[aaronh]

$ set
Apple_PubSub_Socket_Render=/tmp/launch-PdMC3B/Render
BASH=/bin/bash
BASH_ARGC=()
BASH_ARGV=()
BASH_LINENO=()
BASH_SOURCE=()
BASH_VERSINFO=([0]="3" [1]="2" [2]="48" [3]="1" [4]="release" [5]="x86_64-apple-darwin11")
BASH_VERSION='3.2.48(1)-release'
CLASSPATH=.:/Users/aaron/Library/Java
COLUMNS=169
COMMAND_MODE=unix2003
DIRSTACK=()
DISPLAY=/tmp/launch-dwl7XD/org.x:0
DYLD_LIBRARY_PATH=/Users/aaron/programs/root-5.32/lib
EDITOR=emacs
EUID=503
GROUPS=()
HISTFILE=/Users/aaron/.bash_history
HISTFILESIZE=10000
HISTSIZE=500
HISTTIMEFORMAT='%Y-%m-%d %H:%M '
HOME=/Users/aaron
HOSTNAME=agamemnon.local
HOSTTYPE=x86_64
IFS=$' \t\n'
LANG=en_US.UTF-8
LD_LIBRARY_PATH=/Users/aaron/programs/root-5.32/lib:/usr/local/mysql/lib
LIBPATH=/Users/aaron/programs/root-5.32/lib
LINES=50
LOGNAME=aaron
MACHTYPE=x86_64-apple-darwin11
MAILCHECK=60
MANPATH=/Users/aaron/programs/root-5.32/man:/Library/Frameworks/EPD64.framework/Versions/Current/share/man:/Library/Frameworks/Python.framework/Versions/Current/share/man:/opt/local/share/man:/usr/share/man:/usr/local/share/man:/usr/X11/man:/usr/local/mysql/man
MKL_NUM_THREADS=1
OLDPWD=/Users/aaron/programs/CNVnator
OLD_ROOTSYS=/Users/aaron/bin/root
OPTERR=1
OPTIND=1
OSTYPE=darwin11
PATH=/Users/aaron/programs/root-5.32/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Users/aaron/programs/GenomeAnalysisTK-1.0.5336:/Users/aaron/programs/novocraft:/Users/aaron/programs/MUMmer3.22:/Users/aaron/bin:/Users/aaron/Dropbox/bin:/Users/aaron/bin/x86_64:/Users/aaron/programs/blast3:/usr/local/mysql/bin
PERL5LIB=/Users/aaron/programs/vcftools_0.1.4a/perl
PIPESTATUS=([0]="2")
PPID=231
PROMPT_COMMAND='update_terminal_cwd; '
PS1='\u:\W '
PS2='> '
PS4='+ '
PWD=/Users/aaron/programs/CNVnator/src
PYTHONPATH=/Users/aaron/programs/root-5.32/lib:/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
ROOTSYS=/Users/aaron/programs/root-5.32
SECURITYSESSIONID=186a5
SHELL=/bin/bash
SHELLOPTS=braceexpand:emacs:hashall:histexpand:history:interactive-comments:monitor
SHLIB_PATH=/Users/aaron/programs/root-5.32/lib
SHLVL=1
SSH_AUTH_SOCK=/tmp/launch-NrEVlu/Listeners
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=299
TERM_SESSION_ID=3AC7B6C9-0A77-4377-8917-9F03FFF1BE39
THIS=bin
TMPDIR=/var/folders/1j/lkx2dg7d7tn6f4t4c6lwmt9r0000gq/T/
UID=503
USER=aaron
_=make
_GOOGLE_GILD_RUNTIME_FRAMEWORK_ABSOLUTE_PATH_=/Library/Google/Frameworks/Gild.framework
__CF_USER_TEXT_ENCODING=0x1F7:0:0
default_manpath=/Library/Frameworks/EPD64.framework/Versions/Current/share/man:/Library/Frameworks/Python.framework/Versions/Current/share/man:/opt/local/share/man:/usr/share/man:/usr/local/share/man:/usr/X11/man:/usr/local/mysql/man
drop=/Users/aaron/bin/root/lib
newpath=/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
p=/Users/aaron/lib:/Users/aaron/Dropbox/lib:/Users/aaron/Dropbox/bin
calc ()
{
awk "BEGIN{ print $* }"
}
drop_from_path ()
{
if test $# -ne 2; then
echo "drop_from_path: needs 2 arguments";
return 1;
fi;
p=$1;
drop=$2;
newpath=`echo $p | sed -e "s;:${drop}:;:;g" -e "s;:${drop};;g" -e "s;${drop}:;;g" -e "s;${drop};;g"`
}
update_terminal_cwd ()
{
local SEARCH=' ';
local REPLACE='%20';
local PWD_URL="file://$HOSTNAME${PWD//$SEARCH/$REPLACE}";
printf '\e]7;%s\a' "$PWD_URL"
}

$ echo $LD_LIBRARY_PATH
/Users/aaron/programs/root-5.32/lib:/usr/local/mysql/lib

$ echo $ROOTSYS
/Users/aaron/programs/root-5.32

$ which root
/Users/aaron/programs/root-5.32/bin/root

$ make clean
$ make
g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c HisMaker.cpp -o obj/HisMaker.o
g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c AliParser.cpp -o obj/AliParser.o
g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c Genotyper.cpp -o obj/Genotyper.o
g++ -pthread -m64 -I/Users/aaron/programs/root-5.32/include -Isamtools -c Genome.cpp -o obj/Genome.o
g++ -pthread -m64 -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Genome.o samtools/libbam.a -L/Users/aaron/programs/root-5.32/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -pthread -lm -ldl
Undefined symbols for architecture x86_64:
"_deflateInit2_", referenced from:
_deflate_block in libbam.a(bgzf.o)
_razf_open_w in libbam.a(razf.o)
"_deflate", referenced from:
_deflate_block in libbam.a(bgzf.o)
_razf_write in libbam.a(razf.o)
__razf_write in libbam.a(razf.o)
_razf_close in libbam.a(razf.o)
"_deflateEnd", referenced from:
_deflate_block in libbam.a(bgzf.o)
_razf_close in libbam.a(razf.o)
"_crc32", referenced from:
_deflate_block in libbam.a(bgzf.o)
"_inflateInit2_", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
__razf_open in libbam.a(razf.o)
"_inflate", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
__razf_read in libbam.a(razf.o)
"_inflateEnd", referenced from:
_bgzf_read_block in libbam.a(bgzf.o)
_razf_close in libbam.a(razf.o)
__razf_open in libbam.a(razf.o)
"_gzclose", referenced from:
_sam_close in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
"_gzdopen", referenced from:
_sam_open in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
"_gzopen", referenced from:
_sam_open in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
___bam_get_lines in libbam.a(bam_import.o)
"_gzread", referenced from:
_ks_getuntil in libbam.a(bam_import.o)
_sam_header_read2 in libbam.a(bam_import.o)
"_inflateReset", referenced from:
_razf_seek in libbam.a(razf.o)
_razf_jump in libbam.a(razf.o)
"_deflateSetHeader", referenced from:
_razf_open_w in libbam.a(razf.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [cnvnator] Error 1

[dmacmillan]

I suggest you try again from scratch. Use the included samtools. I am not familiar with the usage of libbam.a or how CNVnator utilizes it. But make sure that it was actually created (inside the samtools folder), did you check to see if it exists? Other than that I don't know what could be causing the problem, but right now I think it might be that if your using an external samtools then it wouldn't have libbam.a included in its source directory. So use the included one and 'make' from inside it and check if libbam.a is there.

[aaronh]

I'm assuming that libbam.a is used to read the bam files. It is definitely there. I also used nm to see if the offending symbol is present and it is:
$ nm samtools/libbam.a |grep deflateInit2
U _deflateInit2_
U _deflateInit2_
The compiled objects are indeed 64 bit:
$ file samtools/bgzf.o
samtools/bgzf.o: Mach-O 64-bit object x86_64

Quite frustrating.

[dmacmillan]

Looks like the problem runs quite deep, and I am not very good with libraries and linking them. You could try including your root/lib in your $PATH, I see you only have root/bin. Try that and if it doesn't work then contact the developer because this problem is most likely beyond me. Kind of a last ditch silly error fix, but who knows, its worth a shot.

-cheers

[aaronh]

For the record, there seems to be a problem linking the libz libraries with OSX but CNVnator works fine if you tell it to ignore the linking problems by adding -Wl,-undefined,dynamic_lookup to the Makefile as:
cnvnator: $(OBJS)
$(CXX) -Wl,-undefined,dynamic_lookup -o $@ $(OBJS) $(SAMLIB) $(ROOTLIBS)

Much thanks to the author, Alex Abyzov, for helping me overcome this odd situation.

[fyusufi]

Hello, I followed the instructions given here and successfully installed root and setup the environment variables. The samtools in CNVnator_v0.2.5/src also compiled successfully.

I'm stuck at the final make step for CNVnator. I get the following error:

~/CNVnator_v0.2.5/src$ make
g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.5\" -o cnvnator obj/cnvnator.o obj/HisMaker.o obj/AliParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a -lz -L/home/faraaz/root/lib -lNet -lCore -lCint -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread
/home/faraaz/root/lib/libCint.so: undefined reference to `dlclose'
/home/faraaz/root/lib/libCint.so: undefined reference to `dlsym'
/home/faraaz/root/lib/libCint.so: undefined reference to `dlopen'
/home/faraaz/root/lib/libCint.so: undefined reference to `dlerror'
/home/faraaz/root/lib/libCore.so: undefined reference to `dladdr'
collect2: ld returned 1 exit status
make: *** [cnvnator] Error 1


I'm running this on Ubuntu 10.04. Can anyone help me to solve this? Thanks very much!

[fyusufi]

Ah I managed to fix my problem after searching around on google for a while.

I added in the term "-ldl" into the makefile so that it looks like this:

ROOTLIBS = -L$(ROOTSYS)/lib -ldl -lNet -lCore -lCint -lRIO -lHist -lGraf -lGraf3d \
-lGpad -lTree -lRint -lMatrix -lPhysics \
-lMathCore -lThread -lGui -pthread

[dmacmillan]

Good to know, thanks for the input!

[shriram]

Unable to install the CNVnator, I get following errors

g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.5\" -I:/nexsan/sbhosle/software/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
In file included from cnvnator.cpp:8:
HisMaker.hh:11:20: error: TFrame.h: No such file or directory
HisMaker.hh:12:18: error: TKey.h: No such file or directory
HisMaker.hh:13:26: error: TApplication.h: No such file or directory
HisMaker.hh:14:19: error: TROOT.h: No such file or directory
HisMaker.hh:15:20: error: TTimer.h: No such file or directory
HisMaker.hh:16:21: error: Getline.h: No such file or directory
HisMaker.hh:17:19: error: TFile.h: No such file or directory
HisMaker.hh:18:19: error: TTree.h: No such file or directory
HisMaker.hh:19:18: error: TH1D.h: No such file or directory
HisMaker.hh:20:18: error: TH2D.h: No such file or directory
HisMaker.hh:21:18: error: TH3D.h: No such file or directory
HisMaker.hh:22:19: error: TMath.h: No such file or directory
HisMaker.hh:23:17: error: TF1.h: No such file or directory
HisMaker.hh:24:19: error: TLine.h: No such file or directory
HisMaker.hh:25:21: error: TCanvas.h: No such file or directory
HisMaker.hh:26:20: error: TStyle.h: No such file or directory
HisMaker.hh:27:27: error: Math/DistFunc.h: No such file or directory
HisMaker.hh:28:22: error: TPRegexp.h: No such file or directory
HisMaker.hh:29:24: error: THashTable.h: No such file or directory
HisMaker.hh:30:20: error: TGraph.h: No such file or directory
In file included from cnvnator.cpp:8:
HisMaker.hh:37: error: 'TString' does not name a type
HisMaker.hh:38: error: 'TString' does not name a type
HisMaker.hh:39: error: 'TString' does not name a type
HisMaker.hh:57: error: 'TString' does not name a type
HisMaker.hh:58: error: 'TString' does not name a type
HisMaker.hh:59: error: 'TString' does not name a type
HisMaker.hh:60: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:60: error: expected ';' before '*' token
HisMaker.hh:61: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:61: error: expected ';' before '*' token
HisMaker.hh:62: error: ISO C++ forbids declaration of 'TH2' with no type
HisMaker.hh:62: error: expected ';' before '*' token
HisMaker.hh:63: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:63: error: expected ';' before '*' token
HisMaker.hh:67: error: ISO C++ forbids declaration of 'TF1' with no type
HisMaker.hh:67: error: expected ';' before '*' token
HisMaker.hh:68: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:68: error: expected ';' before '*' token
HisMaker.hh:71: error: ISO C++ forbids declaration of 'TCanvas' with no type
HisMaker.hh:71: error: expected ';' before '*' token
HisMaker.hh:84: error: 'TString' has not been declared
HisMaker.hh:87: error: 'TH1' has not been declared
HisMaker.hh:87: error: 'TH1' has not been declared
HisMaker.hh:88: error: 'TH1' has not been declared
HisMaker.hh:88: error: 'TH1' has not been declared
HisMaker.hh:89: error: 'TH1' has not been declared
HisMaker.hh:89: error: 'TH1' has not been declared
HisMaker.hh:93: error: 'TH1' has not been declared
HisMaker.hh:93: error: 'TH1' has not been declared
HisMaker.hh:94: error: 'TH1' has not been declared
HisMaker.hh:94: error: 'TH1' has not been declared
HisMaker.hh:95: error: 'TH1' has not been declared
HisMaker.hh:95: error: 'TH1' has not been declared
HisMaker.hh:100: error: 'TH1' has not been declared
HisMaker.hh:100: error: 'TH1' has not been declared
HisMaker.hh:100: error: 'TH1' has not been declared
HisMaker.hh:101: error: 'TH1' has not been declared
HisMaker.hh:101: error: 'TH1' has not been declared
HisMaker.hh:101: error: 'TH1' has not been declared
HisMaker.hh:104: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:104: error: expected ';' before '*' token
HisMaker.hh:105: error: ISO C++ forbids declaration of 'TH1' with no type
HisMaker.hh:105: error: expected ';' before '*' token
HisMaker.hh:109: error: 'TString' does not name a type
HisMaker.hh:110: error: 'TString' does not name a type
HisMaker.hh:111: error: 'TString' does not name a type
HisMaker.hh:112: error: 'TString' does not name a type
HisMaker.hh:113: error: 'TString' does not name a type
HisMaker.hh:117: error: 'TString' does not name a type
HisMaker.hh:118: error: 'TString' does not name a type
HisMaker.hh:119: error: 'TString' does not name a type
HisMaker.hh:120: error: 'TString' does not name a type
HisMaker.hh:121: error: 'TString' does not name a type
HisMaker.hh:122: error: 'TString' does not name a type
HisMaker.hh:123: error: 'TString' does not name a type
HisMaker.hh:124: error: 'TString' does not name a type
HisMaker.hh:126: error: 'TH1' has not been declared
HisMaker.hh:139: error: ISO C++ forbids declaration of 'TTree' with no type
HisMaker.hh:139: error: expected ';' before '*' token
HisMaker.hh:150: error: 'TH1' has not been declared
HisMaker.hh:150: error: 'TH1' has not been declared
HisMaker.hh:150: error: 'TH2' has not been declared
HisMaker.hh:150: error: 'TH1' has not been declared
HisMaker.hh:151: error: 'TH1' has not been declared
HisMaker.hh:151: error: 'TH1' has not been declared
HisMaker.hh:151: error: 'TH2' has not been declared
HisMaker.hh:151: error: 'TH1' has not been declared
HisMaker.hh:165: error: 'TString' has not been declared
HisMaker.hh:168: error: 'TString' has not been declared
HisMaker.hh:168: error: 'TString' has not been declared
HisMaker.hh:169: error: 'TVirtualPad' has not been declared
HisMaker.hh:169: error: 'TH1' has not been declared
HisMaker.hh:169: error: 'TH1' has not been declared
HisMaker.hh:169: error: 'TH1' has not been declared
HisMaker.hh:170: error: 'TH1' has not been declared
HisMaker.hh:170: error: 'TH1' has not been declared
HisMaker.hh:171: error: 'TString' has not been declared
HisMaker.hh:172: error: 'TString' has not been declared
HisMaker.hh:172: error: 'TString' has not been declared
HisMaker.hh:172: error: 'TString' has not been declared
HisMaker.hh:172: error: 'TString' has not been declared
HisMaker.hh:178: error: ISO C++ forbids declaration of 'TF1' with no type
HisMaker.hh:178: error: expected ';' before '*' token
HisMaker.hh:188: error: 'TH1' has not been declared
HisMaker.hh:198: error: 'TH1' has not been declared
cnvnator.cpp: In function 'int main(int, char**)':
cnvnator.cpp:86: error: 'TString' was not declared in this scope
cnvnator.cpp:86: error: expected `;' before 'tmp'
cnvnator.cpp:87: error: 'tmp' was not declared in this scope
cnvnator.cpp:92: error: 'tmp' was not declared in this scope
cnvnator.cpp:186: error: 'TApplication' was not declared in this scope
cnvnator.cpp:186: error: expected `;' before 'theApp'
cnvnator.cpp:188: error: 'theApp' was not declared in this scope
cnvnator.cpp:192: error: 'TApplication' was not declared in this scope
cnvnator.cpp:192: error: expected `;' before 'theApp'
cnvnator.cpp:194: error: 'theApp' was not declared in this scope
cnvnator.cpp:212: error: 'TApplication' was not declared in this scope
cnvnator.cpp:212: error: expected `;' before 'theApp'
cnvnator.cpp:214: error: 'theApp' was not declared in this scope
make: *** [obj/cnvnator.o] Error 1

Thanks,
Shriram


Issue has been solved, it was problem with LD_LIBRAY_PATH and ROOTSYS

[Rubal7]

Thanks dmacmillan, this made my life so much easier!