error Installing: CMake fail line 94; RapMap not found (with workaround)

[warrenmcg]

Hi,

First of all, thank you very much for this tool! I'm excited to try it after reading your bioRxiv paper and your blog post. Following your installation instructions, I got to the step where I run CMake [flags] .., and it failed with the following error:

CMake Error at src/CMakeLists.txt:94 (add_executable):
  Cannot find source file:

    /home/wulab2015linux/warren/Software/salmon/external/install/src/rapmap/RapMapFileSystem.cpp

  Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
  .hxx .in .txx

I realized that I did not have curl installed (I use wget all of the time, on a Ubuntu 14.04.4 system), so the fetchRapMap.sh script failed. I tried rerunning the Cmake command after installing curl with apt-get, and it still failed. However, the script worked after I manually ran fetchRapMap.sh, and the build was fine after that.

I'm a complete noob when it comes to CMake files, so I don't know what happened, but I wanted to bring this to your attention and provide users that might have the same issue with a workaround.

[mdshw5]

CMake caches some information during the build in CMakeCache.txt (I think) so you probably have to delete that, or your build directory, and then start again.

[warrenmcg]

I see! Thanks for the tip!

At this point, I would say that there either needs to be a check that curl is installed before using it (for user-friendliness) or that this is a known issue with the workaround above (with the caveat that you delete the CMakeCache.txt file in the build directory after you run fetchRapMap.sh manually). I'm surprised curl is not included with the default developer tools on Ubuntu...

[rob-p]

Hi @warrenmcg — Thanks for your interest in Salmon. There are actually a number of improvements since the pre-print as well! I'm very surprised as well that curl is not available by default on Ubuntu 14.04 (or some variants of the installation). It's actually a very common tool. One thing worth noting is that we also provide pre-compiled binaries for Linux and OSX, if users aren't looking for the "bleeding-edge" version of Salmon, or if their environment causes difficulty in compiling.

[mdshw5]

+1 for curl not being installed on some Linux distros I've used in the past. It's always a shock, but usually there's wget to fall back on, so maybe that's an option for your script...