This page was last updated on Thursday, 06-Mar-2014 09:48:50 CST

Installation notes for TIGRA-SV version 0.1.3.3-6-g715dda8-unstable-dirty

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Note - this is no longer being developed, see also TIGRA install notes

Prerequisites

• From the README file:
  "Since TIGRA-SV uses samtools C API. Please install samtools (http://samtools.sourceforge.net/). Please also modify the Makefile to link the compiler to the correct locations of samtools in your system."

Installation

1. $ cd /programinstallers/
2. $ wget -N https://apt.genome.wustl.edu/ubuntu/files/install.sh
3. Supplied instructions on the web site seem to be out of date. Install from source
   $ git clone --recursive https://github.com/genome/tigra-sv.git
4. $ cd tigra-sv
   The file INSTALL.md contains some instructions
5. Samtools installed previously, see Samtools install notes
   Note Will not compile with samtools version 0.1.19 (see * footnote for error message), but version 0.1.18 worked.
   The current version of samtools libraries and headers is in /usr/lib/samtools,
   and I have the earlier version in /usr/lib/samtools-0.1.18
6. The instruction
   $ export SAMTOOLS_ROOT=/usr/lib/samtools/
   did not work.
   So, and maybe this is not the best way, I had success by following the instruction in the README file:
   "also modify the Makefile to link the compiler to the correct locations of samtools in your system"
7. $ nano CMakeLists.txt
   ...
   # TODO: replace with FindSamtools.cmake
   set(SAMTOOLS_INC /usr/lib/samtools-0.1.18gsc/pkg/bio/samtools/samtools-0.1.6)
   set(SAMTOOLS_LIB /usr/lib/samtools-0.1.18gsc/pkg/bio/samtools/samtools-0.1.6)
   include_directories(${SAMTOOLS_INC})
   link_directories(${SAMTOOLS_LIB})
   ...
8. We will install to /usr/local/bin, the /bin is appended automatically though
   $ cmake . -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
9. $ make
10. I installed manually under a different name, since this is the obsolete version (see TIGRA)
    $ mv bin/tigra-sv /usr/local/bin/tigra-sv-0.1
11. Cleanup
    $ cd ..
12. $ rm tigra-sv -rf

* Error message seen when using executing make with Samtools 0.1.19 libraries and headers:
…

Linking CXX executable ../../../../bin/tigra-sv
/usr/lib/samtools/libbam.a(bgzf.o): In function `bgzf_mt':
/programinstallers/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
/usr/lib/samtools/libbam.a(bgzf.o): In function `mt_destroy':
/programinstallers/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/tigra-sv] Error 1
make[1]: *** [build/src/exe/tigra-sv/CMakeFiles/tigra-sv.dir/all] Error 2
make: *** [all] Error 2