Re: [svtoolkit-help] installing svtoolkit on mac lion - installtest fails

[Bob H. <han...@br...>]

Hi, Adalgeir,

Genome STRiP is pretty computationally intensive, so depending on what 
analysis you are trying to do, you may not get very far without a 
compute cluster.
Partly for this reason, we don't have the resources allocated to support 
non-Linux platforms.

However, if you need to run on mac, bwa is not required for all analyses 
you might want to do with Genome STRiP.
Bwa is used to build the genome masks, but if you are using one of the 
pre-built masks, then this is not an issue (or perhaps you can build the 
mask on a linux box).
Secondly, bwa is used for bulk realignment of unmapped reads to 
breakpoint junctions.
If you are not genotyping known variants (e.g. from 1000 Genomes) with 
assembled breakpoints, then you don't need to use bwa.
Even if you are using breakpoints in genotyping, if you have longer 
reads (e.g. 100bp) and these were aligned to the reference with any 
recent version of bwa,
the contribution from SVAltAlign is usually not very important. It is 
more important with older short reads (< 75bp).

If you do not run the parts of the installtest that include SVAltAlign.q 
and remove -altAlignments from the genotyping, then the installtest 
should run,
although it may produce different results.

Hope this helps,
-Bob

On 6/21/12 11:51 AM, Aðalgeir Arason wrote:
> Hi,
>
> First thanks for making svtoolkit available. I wonder if I can ask 
> your help / advice with installing svtoolkit 1.03.619 on Unix in Mac 
> OS X Lion (10.7.4). Just in brief (details below):
>
> When running the installtests, both fail. The major error seems to be 
> an UnsatisfiedLinkError (no bwa in java.library.path). I tried a 
> solution which in a gsa discussion thread 7 months ago 
> (_https://getsatisfaction.com/gsa/topics/no_bwa_in_java_library_path_) 
> was said to work but didn't explain in enough details for me. It was 
> based on building some mac library, with the aid of a build_mac.sh in 
> GATK/Sting, but I got stuck with finding a location for -lsupc++. I 
> added a comment to the thread and was adviced to contact the svtoolkit 
> authors.
>
> In more detail:
>
> 1) discovery.sh almost worked: I ran the installtest/discovery.sh, 
> resulting in test reasults not matching benchmark data. The 
> discrepancy seemed minimal: A GSDEPTHRANKSUMPVALUE in the bottom 
> paragraph (under DEL_5) was 0.0089357_81_ in my test.1.discovery.vcf 
> whereas it was 0.0089357_8_ in the original vcf in the benchmark 
> folder. Everything else was identical (except the ##fileDate and 
> ##source).
>
> 2) genotyping.sh delivered 'Done with errors' and 'Exception in thread 
> "main" java.lang.UnsatisfiedLinkError: no bwa in java.library.path".
>
> 3) Following the clue in the above mentioned discussion thread, I 
> found build_mac.sh in my GATK/Sting/public/c/bwa folder. I modified an 
> export BWA_HOME command in accordance with the bwa location on my 
> computer, so the bash file contained:
>
>
> #!/bin/sh
> export BWA_HOME=*"/usr/local/bin"*
> export JAVA_INCLUDE="/System/Library/Frameworks/JavaVM.framework/Headers"
> export TARGET_LIB="libbwa.dylib"
> export EXTRA_LIBS="-lc -lz -lsupc++"
> export LIBTOOL_COMMAND="libtool -dynamic"
> make
>
> I have no clue how I should modify other lines (target / extra libs 
> etc), if they are to be adjusted. My JAVA_INCLUDE Headers folder 
> exists in the above location.
>
> The content of the Makefile was:
>
>
> CXX=g++
> CXXFLAGS=-g -Wall -O2 -m64 -fPIC
>
> .cpp.o:
> $(CXX) -c $(CXXFLAGS) -I$(BWA_HOME) -I$(JAVA_INCLUDE) $< -o $@
>
> all: init lib
>
> init:
> @echo Please make sure the following platforms are set correctly on 
> your machine.
> @echo BWA_HOME=$(BWA_HOME)
> @echo JAVA_INCLUDE=$(JAVA_INCLUDE)
> @echo TARGET_LIB=$(TARGET_LIB)
> @echo EXTRA_LIBS=$(EXTRA_LIBS)
> @echo LIBTOOL_COMMAND=$(LIBTOOL_COMMAND)
>
> lib: org_broadinstitute_sting_alignment_bwa_c_BWACAligner.o bwa_gateway.o
> $(LIBTOOL_COMMAND) $? -o $(TARGET_LIB) -L$(BWA_HOME) -lbwacore 
> $(EXTRA_LIBS)
>
> clean:
> rm *.o libbwa.*
>
> I ran the build_mac.sh in the above mentioned Sting directory and it 
> delivered:
>
> Please make sure the following platforms are set correctly on your 
> machine.
> BWA_HOME=/usr/local/bin/bwa
> JAVA_INCLUDE=/System/Library/Frameworks/JavaVM.framework/Headers
> TARGET_LIB=libbwa.dylib
> EXTRA_LIBS=-lc -lz -lsupc++
> LIBTOOL_COMMAND=libtool -dynamic
> libtool -dynamic 
> org_broadinstitute_sting_alignment_bwa_c_BWACAligner.o bwa_gateway.o 
> -o libbwa.dylib -L/usr/local/bin/bwa -lbwacore -lc -lz -lsupc++
> libtool: can't locate file for: -lbwacore
> libtool: file: -lbwacore is not an object file (not allowed in a library)
> libtool: can't locate file for: -lsupc++
> libtool: file: -lsupc++ is not an object file (not allowed in a library)
> make: *** [lib] Error 1
>
> Running the command locate *supc++* results with 
>  /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.6.sdk/usr/lib/libsupc++.a 
> and nothing else. I'm not clear if it means that supc++ is installed. 
> My Xcode is a recent update to 4.3.2. The command locate *lbwa* 
> doesn't find anything.
>
> This is where I'm stuck. I would be most grateful if you could take a 
> look at this and tell if you see what's wrong. Maybe I'm heading the 
> opposite direction trying, the above bash file? I'm relatively new to 
> Unix/Linux and Java.
>
> Thanks again,
>
> Adalgeir
>
>
>
> ---
> Adalgeir Arason
> Landspitali University Hospital
> Reykjavik
> Iceland
>
>
>
> Fyrirvari / Disclaimer
> http://www.landspitali.is/disclaimer/
>
>
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