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

[Aðalgeir A. <ada...@la...>]

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 0.008935781 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/