Install error

[jayramr]

Hi,

I tried below steps

git clone https://github.com/hillerlab/GenomeAlignmentTools.git
cd GenomeAlignmentTools/kent/src
make

cc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib   -o pipeline.o -c pipeline.c
cc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib   -o portimpl.o -c portimpl.c
cc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib   -o pngwrite.o -c pngwrite.c
pngwrite.c:7:10: fatal error: png.h: No such file or directory
    7 | #include "png.h"   // MUST come before common.h, due to setjmp checking  in pngconf.h
      |          ^~~~~~~
compilation terminated.
make[1]: *** [../inc/common.mk:420: pngwrite.o] Error 1
make[1]: Leaving directory '/data/install/genomicallingments/GenomeAlignmentTools/kent/src/lib'
make: *** [makefile:9: topLibs] Error 2

Please advise what I'm missing. Is there any prerequisite to install ?

Thanks
Jay

[jayramr]

I added below

sudo apt-get install libpng-dev libssl-dev

After i ran make

cc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib   -o uuid.o -c uuid.c
In file included from uuid.c:9:
../inc/uuid.h:8:10: fatal error: uuid/uuid.h: No such file or directory
    8 | #include <uuid/uuid.h>
      |          ^~~~~~~~~~~~~
compilation terminated.

Then i installed

sudo apt-get install uuid-dev

Now the make is progressing

[jayramr]

Finally getting below error

/usr/bin/ld: (.text+0x45b): undefined reference to `WPACKET_start_sub_packet_len__'
/usr/bin/ld: (.text+0x484): undefined reference to `WPACKET_close'
/usr/bin/ld: (.text+0x494): undefined reference to `WPACKET_close'
/usr/bin/ld: (.text+0x4a9): undefined reference to `WPACKET_get_total_written'
/usr/bin/ld: (.text+0x4b9): undefined reference to `WPACKET_finish'
/usr/bin/ld: (.text+0x892): undefined reference to `WPACKET_cleanup'
collect2: error: ld returned 1 exit status
make[2]: *** [../../../inc/userApp.mk:31: ../../../../bin//axtChain] Error 1
make[2]: Leaving directory '/data/install/genomicallingments/GenomeAlignmentTools/kent/src/hg/mouseStuff/axtChain'
make[1]: *** [makefile:48: axtChain.all] Error 2
make[1]: Leaving directory '/data/install/genomicallingments/GenomeAlignmentTools/kent/src/hg/mouseStuff'
make: *** [makefile:22: userApps] Error 2

but now no clue only it throwing on /usr/bin/ld

Please advise

[MichaelHiller]

Hi Jay,
axtChain is part of the UCSC kent src code.
We tried to provide a minimal kent src such that people don't have to install the entire kent repo. But apparently, this is hard, as kent has a lot of dependencies.

Maybe it is best to require that https://github.com/ucscGenomeBrowser/kent is properly installed. Afterwards, compiling our chainCleaner chainNet and scoreChain should work, as they are using libs from kent.