Pindel And Mac Os X

Question

[Raygozak]

Has anyone been able to compile Pindel for Mac OS?, it is a great tool but i can't get it to compile under os x.

[Alex Reynolds]

What error messages do you get? It looks like there are a few dependencies, at least libraries from samtools and the klib library - perhaps others - which you'd need to build and install separately. Post error messages and let's see what you find.

Answer 1

[Raygozak]

Just for reference, what i did based on liangkaiye's suggestion was to install homebrew and install the following formula

brew install --enable-cxx --enable-fortran https://raw.github.com/Homebrew/homebrew-dupes/master/gcc.rb

after this, I defined the $(CXX) in the src/Makefile for g++-4.7 and it worked. Hope this helps someone.

Answer 2

[liangkaiye]

Pindel is developed under Mac OS. so sure you can compile it as well for os x.

you just need to get the source code, go to trunk folder and then type

./INSTALL /path/to/

Let me know if you have any questions.

Kai

[Raygozak]

The problem is that it can't find the omp.h header and clearly i have it since i develop with openmp, but for some reason it complains about it, i searched if someone had the same problem in general but couldn't solve it. I have mac os 10.7.5.

[Malachi Griffith]

I have the same problem: clang: warning: argument unused during compilation: '-fopenmp' pindel.cpp:28:10: fatal error: 'omp.h' file not found

This is on a Mac OS 10.7.5 with Xcode 4.5.2 and with Xcode CLI installed and cppcheck installed by homebrew...

[coldrecd]

I'm having a similar problem compiling pindel-0.2.5 on Mac OS

my system:

• OSX 10.9.3
• gcc47 (via homebrew)
• samtools 0.1.18 (locally compiled)
• Cppcheck 1.65

after compiling and checking samtools I added "CXX=gcc47" to pindel-0.2.5/src/Makefile next, make SAMTOOLS=/Users/coldrecd/source/samtools-0.1.18 appears to proceed normally then, ./INSTALL /Users/coldrecd/source/samtools-0.1.18 proceeds with only a few warnings, but ends with

gcc  -Wall -g -c -O3 -fopenmp -I/Users/coldrecd/source/samtools-0.1.18/ genotyping.cpp -o genotyping.o
gcc  pindel.o reader.o reporter.o searcher.o parameter.o refreader.o control_state.o search_deletions_nt.o search_inversions.o search_inversions_nt.o bam2depth.o search_tandem_duplications.o search_tandem_duplications_nt.o output_sorter.o farend_searcher.o search_variant.o searchshortinsertions.o searchdeletions.o output_file_data.o bddata.o shifted_vector.o read_buffer.o line_reader.o ifstream_line_reader.o gz_line_reader.o pindel_read_reader.o user_defined_settings.o fn_parameters.o logstream.o search_MEI_util.o search_MEI.o assembly.o genotyping.o -O3 -fopenmp -lm -lz -L/Users/coldrecd/source/samtools-0.1.18/ -lbam -o pindel
Undefined symbols for architecture x86_64:
...
  "___gxx_personality_v0", referenced from:
      Dwarf Exception Unwind Info (__eh_frame) in pindel.o
      Dwarf Exception Unwind Info (__eh_frame) in reader.o
      Dwarf Exception Unwind Info (__eh_frame) in reporter.o
      Dwarf Exception Unwind Info (__eh_frame) in searcher.o
      Dwarf Exception Unwind Info (__eh_frame) in parameter.o
      Dwarf Exception Unwind Info (__eh_frame) in refreader.o
      Dwarf Exception Unwind Info (__eh_frame) in control_state.o
      ...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [pindel] Error 1
make: *** [pindel] Error 2

I've tried several permutations: pindel-master, samtools st-final, 0.1.19, skipping the initial "make SAMTOOLS..." step, etc, with no luck. I'm getting great results from pindel running on Ubuntu, but I'd really like to get it working on my mac as well.

[liangkaiye]

please use samtools 0.1.18. 0.1.19 does not work for Pindel. You need to download samtools source code and make.

on mac, you need to have gcc installed and set up properly. please fellow the instruction at http://www.ficksworkshop.com/blog/14-coding/65-installing-gcc-on-mac to download gcc and install. Recently mac does not provide a valid gcc by default.

Kai

[roysomak4]

Thanks Kai. It installed like a charm. I am using mac OSX 10.10.

I setup the gcc and g++ compilers as you indicated in the link (http://www.ficksworkshop.com/blog/14-coding/65-installing-gcc-on-mac) followed by downloading and compiling samtools 0.1.18. I then compiled pindel directing to the samtools folder and everything went well.

Note: downloading and compiling older version of samtools had no effect on my working version of samtools.

Answer 3

[liangkaiye]

I also experienced the same problem when I upgraded my mac system. I simply removed xcode and installed a standalone g++, everything works fine.

Malachi, you can visit me at TGI if you have any question about Pindel. my email is kye@genome.

Kai

[ryan.hartmaier]

Hi Kai, I am struggling to get this working. I followed the install instructions and ran ./INSTALL but kept getting a series of fatal errors looking for khash.h opm.h and bam.h. I am running OSX 10.8.3. I installed samtools (v 0.1.19) via homebrew. I also tried uninstalling Xcode like you just suggested without luck.

[Raygozak]

Look on my suggestion on how i fixed it. for samtools you have to download the source, compile it and then give the install the path to this folder, you can delete it afterwards.

Answer 4

[guangxujin]

Just installed the pindel. It took a long time to figure out the issues.

See this link for the process of installment: https://ngsguangxujin.blogspot.com/2017/08/compile-pindel-in-macos.html