Installation on Ubuntu 16.04

[skbrimer]

I know that the development on this only supports upto 14, however I am attempting to get it on the 16 release and I'm having an issue with the build.

Determining if the pthread_create exist failed with the following output:
Change Dir: /opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_2928f/fast"
/usr/bin/make -f CMakeFiles/cmTC_2928f.dir/build.make CMakeFiles/cmTC_2928f.dir/build
make[1]: Entering directory '/opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_2928f.dir/CheckSymbolExists.c.o
/usr/bin/cc    -o CMakeFiles/cmTC_2928f.dir/CheckSymbolExists.c.o   -c /opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_2928f
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2928f.dir/link.txt --verbose=1
/usr/bin/cc      -rdynamic CMakeFiles/cmTC_2928f.dir/CheckSymbolExists.c.o  -o cmTC_2928f
CMakeFiles/cmTC_2928f.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0x1b): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_2928f.dir/build.make:97: recipe for target 'cmTC_2928f' failed
make[1]: *** [cmTC_2928f] Error 1
make[1]: Leaving directory '/opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_2928f/fast' failed
make: *** [cmTC_2928f/fast] Error 2

File /opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef pthread_create
  return ((int*)(&pthread_create))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_2a916/fast"
/usr/bin/make -f CMakeFiles/cmTC_2a916.dir/build.make CMakeFiles/cmTC_2a916.dir/build
make[1]: Entering directory '/opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_2a916.dir/CheckFunctionExists.c.o
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_2a916.dir/CheckFunctionExists.c.o   -c /usr/share/cmake-3.9/Modules/CheckFunctionExists.c
Linking C executable cmTC_2a916
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2a916.dir/link.txt --verbose=1
/usr/bin/cc  -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_2a916.dir/CheckFunctionExists.c.o  -o cmTC_2a916 -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_2a916.dir/build.make:97: recipe for target 'cmTC_2a916' failed
make[1]: *** [cmTC_2a916] Error 1
make[1]: Leaving directory '/opt/software/TS/build/Analysis/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_2a916/fast' failed
make: *** [cmTC_2a916/fast] Error 2

The error code clearly stats it can not locate lpthreads... but neither can I. I'm clearly just missing a dependency but I don't know which one it is. Can you please tell me the package I need to load?

[ipan]

For 16.04, you can build with docker image:

cd /opt/software/TS
docker run -v $(pwd):/src iontorrent/tsbuild:16.04 Analysis

By the default, the docker image run as ionadmin. If the server does not have ionadmin user account, you need to add -u root option to run command.

docker run -u root -v $(pwd):/src iontorrent/tsbuild:16.04 Analysis

[alexyfyf]

The docker way doesn't work for me on 18.04 with gcc 7.3.0. The error message shows fail in bamtools compiling. But I found the latest bamtools already fixed the problem with gcc > 6. So do you need to update some tools @ipan ?