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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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error in old rhel5 #39

Open habibr opened 9 years ago

habibr commented 9 years ago

Hi, I tried to install the latest jellyfish by downloading the release from git. However, I could not find any executable: configure that I can use to invoke the ./configure command.

I tried autoreconf after commenting the binding part and several others.

Then ./configure produced the following: ... checking for _NSGetExecutablePath... no checking execinfo.h ext/stdio_filebuf.h usability... no checking execinfo.h ext/stdio_filebuf.h presence... no checking for execinfo.h ext/stdio_filebuf.h... no configure: error: cannot find required header execinfo.h ext/stdio_filebuf.h

What is this? Where can I find execinfo.h ext/stdio_filebuf.h?

gmarcais commented 9 years ago

Hi,

the configure script is NOT in the git tree. And you should not have to comment anything out of the configure.ac file. The binding part, for example, is enabled by the --enable-swig switch.

You should instead download the release source code, which contains everything needed to compile (https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz)

RedHat 5 ships with very old compilers, you need gcc version >= 4.4. The following should work:

sudo yum install gcc44-c++
./configure CXX=g++44

Hope this helps.