filterBam

[francicco]

Hi,

I'm having problems compiling filterBam

mkdir -p bin
cd src && make CC=cc CXX=g++
make[1]: Entering directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/src'
echo "-Wall -Wno-sign-compare -ansi -pedantic -O3  " > cflags
make[1]: Leaving directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/src'
cd auxprogs && make CC= CXX= BAMTOOLS=
make[1]: Entering directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs'
#cd bam2hints; make CXX= CC= BAMTOOLS=;
#cd compileSpliceCands; make CXX= CC=;
cd filterBam; make CXX= CC= BAMTOOLS=;
make[2]: Entering directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs/filterBam'
(cd src;make CXX= CC= BAMTOOLS=)
make[3]: Entering directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs/filterBam/src'
std=c++0x -c filterBam.cc -o filterBam.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [filterBam.o] Error 127 (ignored)
std=c++0x -c functions/MatePairs.cc -o MatePairs.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [MatePairs.o] Error 127 (ignored)
std=c++0x -c functions/getReferenceName.cc -o getReferenceName.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [getReferenceName.o] Error 127 (ignored)
std=c++0x -c functions/initOptions.cc -o initOptions.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [initOptions.o] Error 127 (ignored)
std=c++0x -c functions/SingleAlignment.cc -o SingleAlignment.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [SingleAlignment.o] Error 127 (ignored)
std=c++0x -c functions/printElapsedTime.cc -o printElapsedTime.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [printElapsedTime.o] Error 127 (ignored)
std=c++0x -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [sumMandIOperations.o] Error 127 (ignored)
std=c++0x -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [sumDandIOperations.o] Error 127 (ignored)
std=c++0x -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/include -Iheaders -I./bamtools 
/bin/sh: -c: command not found
make[3]: [PairednessCoverage.o] Error 127 (ignored)
std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam /lib/libbamtools.a -lz 
/bin/sh: filterBam.o: command not found
make[3]: [filterBam] Error 127 (ignored)
[Makefile]: ${BAMTOOLS} has not been set.
make[3]: *** [CHECKBAM] Error 101
make[3]: Leaving directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs/filterBam/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs/filterBam'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/rds/user/fc464/hpc-work/SoftwareTwo/augustus/auxprogs'
make: *** [all] Error 2

[nextgenusfs]

It’s looking for BAMTOOLS variable, pass it to make with BAMTOOLS=/path/to/BAMTOOLS or edit makefile in the filterbam script. It looks like you are on Linux- the district here is for Mac. You should be able to install with bioconda or a variety of other methods on Linux.

[francicco]

I'm really close to solve this. I don't really understand what -lbamtools is pointing at.
I have libbamtools.a libbamtools.so libbamtools.so.2.3.0 in the lib64 folder within bamtools

make[2]: Entering directory `/home/fc464/software/Augustus/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory `/home/fc464/software/Augustus/auxprogs/filterBam/src'
g++     -std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -l/home/fc464/software/Augustus/bamtools/lib64/libbamtools.a -lz 
/usr/bin/ld: cannot find -l/home/fc464/software/Augustus/bamtools/lib64/libbamtools.a
collect2: error: ld returned 1 exit status

[nextgenusfs]

Look at how I modified makefile for macOS https://github.com/nextgenusfs/augustus/blob/master/auxprogs/filterBam/src/Makefile

[francicco]

Done it! Now I'm struggling with lp_solve libraries... F

…

On Fri, 21 Sep 2018, 14:03 Jon Palmer, ***@***.***> wrote: Look at how I modified makefile for macOS https://github.com/nextgenusfs/augustus/blob/master/auxprogs/filterBam/src/Makefile — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIlvFnaZUjMgUeEamSWu4HS3uF4aby_xks5udOO-gaJpZM4WygIk> .