Error installing on MacOS

[Asutu]

Hi,

I'm trying to compile mergeSVcallers with:

git clone --recursive https://github.com/zeeev/mergeSVcallers.git
cd mergeSVcallers
make

but always got the following error:

...

c++ -O3 -c -o Repeats.o Repeats.cpp -I.
c++ -O3 -c -o IndelAllele.o IndelAllele.cpp -I.
c++ -O3 smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o -I. -o smithwaterman
ld -r BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o -o sw.o -L.
INFO: set seqid region to : BandedSmithWaterman.o
ld: invalid option -- o
ld: invalid option -- L
ld: invalid option -- .
FATAL: failed to specify genotype likelihood format : PL or GL

INFO: help
INFO: description:
INFO: LD --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf -e -d -r                                           

INFO: required: t,target     -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns        
INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns    
INFO: required: f,file       -- argument: a properly formatted phased VCF file                                                       
INFO: required: y,type       -- argument: type of genotype likelihood: PL, GL or GP                                                  
INFO: optional: w,window     -- argument: window size to average LD; default is 1000                                                 
INFO: optional: e,external   -- switch: population to calculate LD expectation; default is target                                    
INFO: optional: d,derived    -- switch: which haplotype to count "00" vs "11"; default "00",                                   

------------------------------------------------------
              This is a vcflib::GPAT++ tool           
-Version       : v1.0.0-rc0-315-g09df
-Contact       : zev.kronenberg [at] gmail.com 
-Notes         : If you find a bug, please open a report on github!
-Support       : Please post questions to biostars.org             
-Contribution  :                                                   
                 Zev Kronenberg (UW Genome Sciences)               
                 Mark Yandell   (UU Human genetics)                
                 Mike Shapiro   (UU Biology)                       
                 EJ Osborne     (UU Human genetics)                
                 Brett Kennedy  (UU Human genetics)                
                 Daniel Ence    (UU Human genetics)                
                 Erik Garrison  (Wellcome Trust Sanger Institute)  
                 Travis Collier (UC Davis)                         
                 -     Your name goes here       -'                
------------------------------------------------------
make[2]: *** [sw.o] Error 1
make[1]: *** [smithwaterman/SmithWatermanGotoh.o] Error 2
make: *** [buildVCFlib] Error 2

I would guess this is related with the branch of the vcflib that comes with mergeSVcallers because I previously installed successfully vclib on my machine (patch 09df564).

I'm running on a Mac:

ProductName:    Mac OS X
ProductVersion: 10.12.4
BuildVersion:   16E195

Any workaround to fix this issue?

Thanks, Pedro

[zeeev]

That is really, really bizarre. Does this happen on clean install?

[Asutu]

No. After removing the path to the previous vcflib install directory from my $PATH variable, mergeSVcallers compiled successfully, so I think the problem is related to the way vcflib is compiled if there's a previous installation of it.

Thanks.