Hi all,

I've just started working with molecular evolution and Hyphy is really new to me as well. Unfortunately I'm neither a linux expert too. Running REL on my windows xp machine on just 36 sequences takes ages to finish. So I'm hoping that the linux version will speed thing up. However, I'm struggling with the installation. Basically I used git to download hyphy and did the following:

$ cmake -DINSTALL_PREFIX=/nfs_netapp2/myusername/hyphy
$ make MP2  #This seemed to run fine
$ make GTEST  #This also seemed to run fine

However when I tried to make the target LIB I got the following error:
...
make[3]: *** [CMakeFiles/hyphy_mp.dir/src/core/batchlanruntime.cpp.o] Error 1
make[2]: *** [CMakeFiles/hyphy_mp.dir/all] Error 2
make[1]: *** [CMakeFiles/LIB.dir/rule] Error 2
make: *** [LIB] Error 2

I'm also having problem installing the GUI version. I did the followings but both ran into errors:

$ make GTK
make: *** No rule to make target `GTK'.  Stop.

$ scripts/gtk_build.sh MP2
Linux
Checking for curl
Curl seems to be present
+-----------------------------------------------------------+
|Building a multi-threaded HYPHYKernelMP with setconcurrency|
+-----------------------------------------------------------+
COMPILER=g++, gcc
COMPILER_FLAGS= -w -c -O3 -D INTPTR_TYPE=long -fsigned-char -fpermissive -I/nfs_netapp2/hzen/bin/software/hyphy/GUI -I/nfs_netapp2/hzen/bin/software/hyphy/Source -I/nfs_netapp2/hzen/bin/software/hyphy/Source/SQLite -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/libpng12    -D GDK_PIXBUF_ENABLE_BACKEND -D __HYPHY_GTK__ -D _SLKP_LFENGINE_REWRITE_  -D __MP__ -D __MP2__ -fopenmp
scripts/gtk_build.sh: line 148: cd: Source: No such file or directory
Building *.cpp
g++: *.cpp: No such file or directory
g++: no input files
Error during compilation

In addition, when I ran the gtest I also got one failed error message which I don't understand:

$ ./HYPHYGTEST
...
[  FAILED  ] 1 test, listed below:
[  FAILED  ] StringTest.AppendAnAssignmentToBufferTest


I'll appreciate any help with my installation problem.

Thank you.

Greetings Rosz,

Please check out from git.

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Make sure you have GTK libraries installed:
yum install gtk2-devel

cd into your hyphy directory:
cmake .
make HYPHYGTK
make install

run:
HYPHYGTK

We have not tested with Scientific Linux, if there are further issues, please let us know and we will take a further look.

Hi Steven,

Thanks for the help. Pulling down the latest update has now allowed me to install the GUI version. However, when I tried to run CodonBivariateRateProcessor.bf, it gave the following errors and nothing happened after that:

** (HYPHYGTK:31988): WARNING **: Invalid borders specified for theme pixmap:
        /nfs_netapp2/hzen/bin/software/hyphy/lib/hyphy/GTKResources/theme/entry1.png,
borders don't fit within the image