Issues with staticallly linked binary from GitHub viral-ngs repo

[Bede Constantinides]

I am getting errors running a statically linked OS X binary obtained from the URL below.
https://github.com/broadinstitute/viral-ngs/tree/master/tools/binaries/V-Phaser-2.0

Any suggestions? Might anyone have a statically linked OS X binary they could share?

```
l-umobcdja2:vp2 Bede$ ./variant_caller -i /Users/Bede/Research/Analyses/sm_nasal/stock.sub100.bam -o stock_sub/

--------------------------------------------------------
Program runs with the following Parameter setting:

    input BAM file    =    /Users/Bede/Research/Analyses/sm_nasal/stock.sub100.bam
    output Directory    =    stock_sub/
    errModel        =    pileup + phase
    alpha        =    0.05
    ignoreBases     =    0
    (var_matepair, var_cycle, var_dt, var_qt)    =    1,1,1,20
    pSample        =    30%
    windowSz    =    500
    delta    =    2

--------------------------------------------------------


    1 bam file(s) found:
        /Users/Bede/Research/Analyses/sm_nasal/stock.sub100.bam


Parse bam header: get refSeq info & sanity check

    gi|221708|dbj|D00239.1|HRVACG len =7133

    1 ref sequence(s) found:
        Name: gi|221708|dbj|D00239.1|HRVACG
            BamfileID = 0    RefID = 0


    0 platform(s) found:


Get maxQ, minQ, maxReadLen, avgFragSz, stdFragSz from bam files ...

    Total Reads = 102648
    # Mapped Reads = 102648
    # Reads used for checking Q scores = 30897
    minQ = 35    maxQ=69        maxRL = 150
    (avgfragSz, std) = 136    178

Generate qual -> quantile map ...


Set up paired read map arrays ...

    # total mapped reads: 102648
    # mapped mate-pairs = 51172

Prepare aln columns file...

 Ref: gi|221708|dbj|D00239.1|HRVACG , len = 7133


        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.0.499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.500.999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.1000.1499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.1500.1999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.2000.2499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.2500.2999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.3000.3499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.3500.3999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.4000.4499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.4500.4999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.5000.5499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.5500.5999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.6000.6499.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.6500.6999.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.7000.7132.region

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.covplot.R
        (#pos, Avg Cov) = (7041, 1983.34)

        create file: stock_sub//gi|221708|dbj|D00239.1|HRVACG.eb

Inference ...


    Calibrate errors...

     LV pe = 2682/15319857 = 0.000175067
     avg bucket size: 651
     SNPV pe = 119098/13962048 = 0.00853012
     avg bucket size: 593

        Iteration 0

        Process stock_sub//gi|221708|dbj|D00239.1|HRVACG.0.499.region
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Users/Bede/Research/Tools/viral_variation/vp2/./libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Users/Bede/Research/Tools/viral_variation/vp2/./libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap: 5
```

[Christopher Tomkins-Tinch]

Sorry to hear you've hit a snag.

If you're looking for only v-phaser2, you might try the binary distributed via the bioconda channel, though the linking for libgomp should be comparable:

https://anaconda.org/bioconda/vphaser2/files

In the newer versions of viral-ngs (>v1.2.0) we have moved to conda-based install of many tools, including v-phaser2.

Both the binary on bioconda and the binary distributed via vial-ngs were build with gcc-4.9.1, and link against that version of libgcc/libstdc++. You might try installing gcc-4.9.1 from Homebrew, as well as boost.