breakdancer help compile and installation

[antoza]

Hi folks,

I am trying to use breakdancer in older to detect structural variations. Actually I faced a lot of problems trying to install it. Initially, I have downloaded breakdancer-1.1_2011_02_21 in my Ubuntu 12 LTS OS and installed all the dependencies needed (like modules Statistics:escriptive, Math::CDF). While I have successfully run the bam2cfg.pl script, using my sorted bam file as input (the output cfg file is as follows:

readgroup:NA platform:illumina map:48_1764FIL.sorted.bam readlen:73.54 lib:NA num:878 lower:0.00 upper:538.62 mean:198.79 std:69.15 SWnormality:-25.23 exe:samtools view), I cant understand how I will later run the perl version.

The content of the breakdancer-1.1_2011_02_21 folder is as follows and I have also difficulties to run the cpp version because is not so clear to me how I will compile and install it. I have previously already installed samtools 0.1.18 in my system from synaptic package manager (their path is as follows: /usr/bin/samtools /usr/lib/samtools /usr/bin/X11/samtools /usr/include/samtools /usr/share/samtools /usr/share/man/man1/samtools.1.gz).

*README

*./cpp:
*AlnParser.cpp
*breakdancer_max
*BreakDancerMax.h
*Poisson.cpp
*samtools.h
*AlnParser.h
*BreakDancerMax.cpp
*Makefile
*Poisson.h

*./perl:
*AlnParser.pm
*bam2cfg.pl
*Poisson.pm


Next try was to download the breakdancer-1.4.1 (https://github.com/genome/breakdancer/releases) but when I read the install.md file according to a much straightforward procedure it says that I have to build breakdancer by installing samtools 0.1.6 (as far as I understand an oldest version of samtools than this I have already installed it) and to export samtools_root to the environment path (export SAMTOOLS_ROOT=$(pwd)). I am quite wondering if there would be any conflict issue in aspects that I have already installed samtools 0.1.18 in my system. I don’t know really how to proceed can somebody make me understand how breakdance will being installed in details.
Many thanks in advance.

[ernfrid]

Hi antoza,

I updated the docs for BreakDancer relatively recently and what you actually need is samtools-0.1.19 or higher for BreakDancer v1.4.0 and up. I apologize that what you grabbed didn't include the proper documentation. I will need to look into how to fix that.

Secondly, downloading the tarball or zip file is going to make your life more complicated. You should just check out the sourcecode directly following the instructions in the INSTALL.md file. To get the last stable release just do: git checkout v1.4.1 after the recursive clone, but before you attempt to compile.

I do think that you will need to grab the samtools sourcecode and compile it, rather than using the debian package. The debian package doesn't install the necessary header files, if I recall correctly. All you need to do is compile samtools, you don't need to install it. BreakDancer uses this samtools at compile time only so it shouldn't conflict with your installed version of samtools.

Hope this helps. Please ask for further clarification if needed.

[antoza]

Dear ernfrid,

Many thanks for your reply and all the clarifications provided. However, I am still a little confused regarding how I will make breakdancer comes to work. In order to follow the instructions in INSTALL.md file I suppose initially I have to download the breakdancer1.4.1.tar.gz file from https://github.com/genome/breakdancer/releases and then extracting its content.

However, I have tested directly to my directory to make a recursive clone as below
$ git clone --recursive https://github.com/genome/breakdancer.git
and then an unnamed “breakdancer” directory is coming out. Then i make the following:
$ cd breakdancer
$ git checkout v1.4.1
It comes something like the following
You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:
git checkout -b new_branch_name
HEAD is now at ad8e3c8... quick fix for fastq writing (cache output filehandles)

At the moment i am here. Is there any wrong with these indications. What I have to do later? In order to compile samtools-0.1.19 I suppose I have to do the next steps inside breakdancer directory.

$ mkdir build
$ cd build
$ wget "http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2"
$ tar -jxvf samtools-0.1.19.tar.bz2
$ cd samtools-0.1.19
$ sudo make

Do I have to export as below
$ export SAMTOOLS_ROOT=$(pwd)

or to copy the compiled libraries to /usr/local/lib as below

$ cp $SAMTOOLS_HOME/libbam.a /usr/local/lib
And then to copy headers to /usr/local/include as below
$ mkdir /usr/local/include/bam
$ cp $SAMTOOLS_HOME/*.h /usr/local/include/bam

Finally I suppose I have to install breakdancer (if everything of the above were made ok) as below:
$ cd ..
$ sudo cmake ..
...
-- Build files have been written to: .../breakdancer/build
$ sudo make
...
Linking CXX executable ../../../../bin/breakdancer-max
[100%] Built target breakdancer-max

$ sudo make install

Could you please clarify (by commands lines if it possible) according to above steps which is the proper procedure to compile the samtools-0.0.19 inside breakdancer build directory and later install breakdancer-1.4.1?
Thanks for you help!!

[ernfrid]

1. Your steps to check out breakdancer look fine. That error message is expected when checking out a tag.
2. I believe you may place the samtools code anywhere you like. I would probably not put it inside breakdancer though as I personally find that confusing. I usually put it in its own directory alongside breakdancer (e.g. I have a directory called src in my home directory and there are src/breakdancer and src/samtools-0.1.19 inside it.
3. Your compilation of samtools looks fine.
4. I would export SAMTOOLS_ROOT as the directions state. (e.g. for my example about export SAMTOOLS_ROOT=~/src/samtools-0.1.19/

From this point forward:

$ cd /path/to/breakdancer
$ mkdir build
$ cd build
$ sudo cmake ..
$ sudo make
$ sudo make install