configure: error: cannot run /bin/sh ./config.sub

[fidelram]

Hi,

When I run ./configure I always get the following message:

configure: error: cannot run /bin/sh ./config.sub

In the configure file I found:

# These three variables are undocumented and unsupported,
# and are intended to be withdrawn in a future Autoconf release.
# They can cause serious problems if a builder's source tree is in a directory
# whose full name contains unusual characters.
ac_config_guess="$SHELL $ac_aux_dir/config.guess"  # Please don't use this var.
ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.

I wonder if perhaps config.sub and config.guess are missing in the repository?

[fidelram]

In case it helps, I manage to pass this issue by typing:

autoreconf --install

before ./configure

[teedeedubya]

@fidelram
Edit again (updating to account for road bumps encountered during "make")

This is exactly what i did, in this order.

• Did a fresh Centos 7 minimal install
• download the following RPM and copy it to your box:
  ftp://rpmfind.net/linux/centos/7.3.1611/os/x86_64/Packages/boost-devel-1.53.0-26.el7.x86_64.rpm
• download epel 7 repository configuration
  https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
• install boost-devel:
  yum --nogpgcheck localinstall boost-devel-1.53.0-26.el7.x86_64.rpm
• install the epel repository
  yum --nogpgcheck localinstall epel-release-latest-7.noarch.rpm
• install samtools-devel and zlib-devel:
  yum install samtools-devel
  yum install zlib-devel
• install some more crap:
  yum install gcc
  yum install unzip
  yum install automake
  yum install make
  yum install gcc-c++
• unpack Lachesis and copy in a couple of needed files:
  unzip LACHESIS-master.zip
  cp /usr/share/automake-1.13/config.guess /root/LACHESIS-master/
  cp /usr/share/automake-1.13/config.sub /root/LACHESIS-master/
  cp /usr/share/automake-1.13/depcomp /root/LACHESIS-master/
• export samtools(I didn't have to export boost)
  export LACHESIS_SAMTOOLS_DIR=/usr/include/samtools/
• configure it
  ./configure --with-samtools=/usr/include/samtools/
• delete artifacts left over in the repository
• source: build failure #28
• Thanks @llinsson
  for i in find /root/LACHESIS-master/ -name "*.[ao]"; do echo -e "Removing ${i}"; rm ${i} ; done;
• i f for whatever reason, it's unable to find sam.h in SAMStepper.h and SAMStepper.cc,
• Modify ./src/include/gtools/SAMStepper.h and ./src/include/gtools/SAMStepper.cc
  from:
  #include <sam.h>
  to:
  #include "/usr/include/samtools/sam.h"
• install it
  make
  make install

Cheers,
Tony

[dpryan79]

This ends up getting solved by #28. It boggles my mind why #28 hasn't been fully implemented in the github repository and the installation instructions updated.