unable to install pb_calibration

[grendon]

I tried installing this tool in two separate clusters without success!
It fails at the same point: when configuration command is checking samtools. Could it be a bug?

1. On Blue Waters
   Blue Waters is a cray-based system. However, the user can switch to a different working environment: gnu programming environment, cluster-compatibility mode, and so on.
   https://bluewaters.ncsa.illinois.edu/cluster-compatibility-mode
   I installed zlib and staden as prerequisites to installing pb_calibration. Yet, I am unable to get it to compile.
   The configure command fails when it checks samtools. Needless to say, our version of samtools is ok and functional. So, I do not know what to do.

This is the scriptlog

rendong@nid25433:/projects/sciteam/jti/builds/pb_calibration/src> ./bootstrap

rendong@nid25433:/projects/sciteam/jti/builds/pb_calibration/src> ./configure --prefix=/projects/sciteam/jti/builds/pb_calibration --with-io_lib=/projects/sciteam/jti/builds/staden-2.0.0b10-compiled --with-zlib=/projects/sciteam/jti/builds/zlib-1.2.8 --with-samtools=/projects/sciteam/jti/builds/samtools-0.1.19 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking CFLAGS for maximum warnings... -Wall checking for inline... inline checking for gcc option to accept ISO C99... -std=gnu99 checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for asprintf... yes checking for pread... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for staden-io_lib-config... no checking for io_lib-config... /projects/sciteam/jti/builds/staden-2.0.0b10-compiled/bin/io_lib-config checking if io_lib version >= 1.12.1... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing bam_header_read... no checking for library containing bam_header_read... no configure: WARNING: --with-samtools specified, but non-functioning checking for library containing bam_header_read... (cached) no checking for library containing bam_header_read... no configure: WARNING: --with-samtools specified, but non-functioning configure: WARNING: No functioning samtools found configure: error: Abort: no samtools. Please rerun configure using the ---with-samtools=DIR option. 1. on a linux-based cluster The IGB biocluster is a linux-based cluster http://help.igb.illinois.edu/Biocluster#Description

I installed staden then I added it to LD_LIBRARY_PATH and C_INCLUDE_PATH.
I loaded these two modules zlib and samtools.
Finally, I tried to install pb_calibration. the configuration command failed!

This is the corresponding scriptlog

[grendon@biocluster src]$ ./configure --prefix=/home/a-m/grendon/bin/pb_calibration --with-samtools=/home/apps/samtools/samtools-0.1.19
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking CFLAGS for maximum warnings... -Wall
checking for inline... inline
checking for gcc option to accept ISO C99... -std=gnu99
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for asprintf... yes
checking for pread... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for staden-io_lib-config... no
checking for io_lib-config... /opt/rocks/bin/io_lib-config
checking if io_lib version >= 1.12.1... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing bam_header_read... no
checking for library containing bam_header_read... none required
checking bam.h usability... no
checking bam.h presence... no
checking for bam.h... no
configure: WARNING: --with-samtools specified, but non-functioning
checking for library containing bam_header_read... (cached) none required
checking for bam.h... (cached) no
checking for library containing bam_header_read... none required
checking for bam.h... (cached) no
configure: WARNING: --with-samtools specified, but non-functioning
configure: WARNING: No functioning samtools found
configure: error: Abort: no samtools. Please rerun configure using the ---with-samtools=DIR option.

[srl147]

I've just downloaded a fresh copy of pb_calibration and successfully complied it against our installed version of samtools-0.1.19. The samtools check is simply looking for bam.h and checking the function bam_header_read exists in the library. Can you confirm the files bam.h and libbam.a exist in your samtools-0.1.19 directory