Between my final year of PhD (when I was also working as IBERS and IMAPS HPC SysAdmin) my life consisted of installing software into a module type system since HPC environments have multiple pieces of software installed, often the same software but with different versions and you fundamentally do not use a package manager for user software as it'll cause you a world of pain. One annoyance I always found was when you look for help when a piece of software fails to compile and you get an answer that boils down to;
yum install PACKAGE
apt-get install PACKAGE
And this happened today. bcl2fastq, the Illumina software is all kinds of fun and games (USING MAKE FILES TO DEMULTIPLEX RAW DATA???? WHY?????). The install instructions are your usual ./configure/make....so you do your ./configure and all is well until you get the following error...
boost-1_44_0 installed successfully -- Successfuly built boost 1.44.0 from the distribution package... -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for floorf -- Looking for floorf - found -- Looking for round -- Looking for round - found -- Looking for roundf -- Looking for roundf - found -- Looking for powf -- Looking for powf - found -- Looking for erf -- Looking for erf - found -- Looking for erf -- Looking for erf - found -- Looking for erfc -- Looking for erfc - found -- Looking for erfc -- Looking for erfc - found CMake Error at cmake/cxxConfigure.cmake:74 (message): No support for gzip compression Call Stack (most recent call first): c++/CMakeLists.txt:33 (include) -- Configuring incomplete, errors occurred! Couldn't configure the project: /software/testing/bcl2fastq/1.8.4/build/bootstrap/bin/cmake -H"/software/testing/bcl2fastq/1.8.4/src/bcl2fastq/src" -B"/software/testing/bcl2fastq/1.8.4/build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH=/software/testing/bcl2fastq/1.8.4/x86_64 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/software/testing/bcl2fastq/1.8.4/x86_64 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo Moving CMakeCache.txt to CMakeCache.txt.removed
My first thought was to quickly look to see if we have libz libraries installed on the HPC as a module, and they're not. Fair enough. I then wondered why there wasn't a libz library already installed by the OS, and there is but it seems to be different between the software node (a node dedicated to installing software so as not to annoy folk who are on the login node) and the compute nodes. So pointing to /lib64 would probably not work (it might if bcl2fastq is doing a static binary, I've not checked).
[[email protected]]$ locate libz /lib64/libz.so.1 /lib64/libz.so.1.2.3
[[email protected]]$ locate libz -bash: locate: command not found [[email protected]]$ echo "grrr" grrr [[email protected]]$ ls -lath /lib64/libz* lrwxrwxrwx 1 root root 13 Dec 13 14:09 /lib64/libz.so.1 -> libz.so.1.2.7 -rwxr-xr-x 1 root root 89K Nov 5 18:09 /lib64/libz.so.1.2.7
Okay so after a quick google I get the same old hacky responses;
My next thought then was how about I just install libz from source. So,
[[email protected]]$ source git-126.96.36.199 [[email protected]]$ which git [[email protected]]$ git clone https://github.com/madler/zlib.git
YES, EVEN GIT HAS VERSIONS!!! yum/apt isn't the answer to everything!
[[email protected] ]$ cd zlib/ [[email protected] ]$ ./configure [[email protected] ]$ make -j4
[[email protected] ]$ ls -lath libz*s*
lrwxrwx--- 1 martin JIC_c1 14 Jan 27 16:11 libz.so.1 -> libz.so.1.2.11
lrwxrwx--- 1 martin JIC_c1 14 Jan 27 16:11 libz.so -> libz.so.1.2.11
-rwxrwx--x 1 martin JIC_c1 103K Jan 27 16:11 libz.so.1.2.11
And that's great. We now have our libraries compiled, just need to let my bash shell know where they are;
and then back into my bcl2fastq build directory, rerun ./configure --prefix=/where/the/bins/go and it compiled.
All done without a yummy apt....it's Friday and I need to go home.