installing strelka v1.0.12 on mac

[Joon]

Hi,

   I am trying to install strelka on my macbook. I've got the following error message and failed to install strelka. Would you please take a look at the error below? Thanks a lot!

Joon

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/redist build

make[1]: Nothing to be done for `build'.

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/src build

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/src/c++ build

make[2]: Nothing to be done for `build'.

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/src/perl build

make[2]: Nothing to be done for `build'.

mkdir -p /Users/joonlee/NGS/strelka_workflow/v1.0.12/bin

mkdir -p /Users/joonlee/NGS/strelka_workflow/v1.0.12/lib

mkdir -p /Users/joonlee/NGS/strelka_workflow/v1.0.12/libexec

STRICT_COMPILE=0 /Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/strelka test

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C /Users/joonlee/Downloads/strelka_workflow-1.0.12/strelka/redist

/Applications/Xcode.app/Contents/Developer/usr/bin/make -C samtools-0.1.18_no_tview && \

ln -sf samtools-0.1.18_no_tview samtools

make[5]: Nothing to be done for `lib'.

make[5]: Nothing to be done for `lib'.

make[5]: Nothing to be done for `lib'.

gcc -g -Wall -O2  -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools  libbam.a -lbcf  -lm -lz

Undefined symbols for architecture x86_64:

  "___ks_insertsort_heap", referenced from:

      _ks_combsort_heap in libbam.a(bam_sort.o)

      _ks_introsort_heap in libbam.a(bam_sort.o)

  "_lseek64", referenced from:

      _knet_seek in libbam.a(knetfile.o)

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[4]: *** [samtools] Error 1

make[3]: *** [all-recur] Error 1

make[2]: *** [samtools] Error 2

make[1]: *** [redist] Error 2

make: *** [test] Error 2

[Saunders, Chris]

Hi Joon –

 

I don’t currently have access to a mac but my understanding is that gcc has been aliased to point to clang starting with XCode 5, which might be contributing to some issue with samtools compilation.

 

I can try to look into this once I have a test system available –in the meantime this information would be helpful:

 

1)      What os x version is this? What does ‘gcc –v’ return?

2)      Do you see the same problem compiling samtools 01.18 on its own? Does the problem still exist in a newer samtools version?

 

Thanks,

 

-Chris

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[Paul Antoniou]

Hello, 

I am having the same error when I try to install on imac with ios 10.10. 

The gcc does point to clang. But I install samtools on the mac with no issues and I am using it on its own. 

Thanks, 

Paul

[Chris Saunders]

Hi Paul,

The best I can do right now is attempt to reproduce the error using the same version of clang on linux, the development version of strelka is working with the newest clang version but perhaps there's something I can patch up on the 1.x version to take care of this. What is the exact compiler version for ios 10?

Best,

-Chris

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[Paul Antoniou]

Hi Chris,

thank you for your reply and apologies for taking so long to get back to you. I have installed g++ from macports so that clang won't no longer be an issue but unfortunately i could not succesfully make Strelka. Again i got the ld:symbol not found for archtecture x86_64 error. Therefore I believe it is not due to clang I was getting the errors before. Will try to find out more. 

Thanks 

Paul

[John Finnigan]

Hello, 

I apologize for resurrecting an old thread, but I am experience the same issue. Did anyone ever identify a solution to this problem? 

Thanks!

Regards,

John

[Saeed Al Turki]

I got the same error but I managed to installed Strelka v1.0.14 on my Mac OS 10.10.4

It seems the failure happens at the samtools step so I replaced Strelka's samtools with the original samtools (same version), changed samtools folder name to match the Makefile and its worked. I ran Strelka demo and it seems to work!

Here are the steps:

# download samtools v0.1.18 and rename its folder them compress the files

wget http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2

tar zxfv samtools-0.1.18.tar.bz2

mv samtools-0.1.18 samtools-0.1.18_no_tview

tar zcvf samtools-0.1.18_no_tview.tar.bz2 samtools-0.1.18_no_tview/

# download Strelka v1.0.14 then replace its version of samtools with the one above

wget ftp://str...@ftp.illumina.com/v1-branch/v1.0.14/strelka_workflow-1.0.14.tar.gz

tar zxfv strelka_workflow-1.0.14.tar.gz

mv samtools-0.1.18_no_tview.tar.bz2 strelka_workflow-1.0.14/strelka/redist/

# processed with installation as per Strelka instructions

cd strelka_workflow-1.0.14

./configure 

make

I hope this helps, 

Saeed

[Saeed Al Turki]

Minor correction:

In the steps I mentioned  in my last email, replace the following line:

tar zcvf samtools-0.1.18_no_tview.tar.bz2 samtools-0.1.18_no_tview/

with this one (use j instead of z)

tar jcvf samtools-0.1.18_no_tview.tar.bz2 samtools-0.1.18_no_tview/

since Strelka's Makefile expects bz2 files.

[Saunders, Chris]

Thanks for sharing these instructions with everyone Saeed!

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