Installing Kallisto (RNA-Seq quantification program) on our Red Hat Cluster

Today I decided to install the RNA-Seq quantification tool Kallisto  for testing, this appears to be a good tool ( detailed here ) and I have high confidence on the underlying theoretical rigor, which usually the bane of any new tool.

Straight awa, I ran into some installation troubles. After troubleshooting for a couple of hours I finally got the tool installed from source. First, I ran into this error using gcc


After googling around a little bit, i found that the version of gcc we have did not support the C++-11 standard  and i had to make sure  we had the latest  gcc modules loaded .. but lo behold the cmake still failed to recognize the newgcc  modules


Some more googling revealed that perhaps i need to change the CC and CXX environment variables and i did that as well to no avail


More googling revealed that there was a catch to all this, apparently to reset cmake variables for the C compiler, the entire build directory needs to be deleted and we should start clean. So I went ahead and deleted the kalissto source folder, and untarred the download and re-ran CMAKE and voila!!! it finally compiled


a word of caution here is that you need to have the $CC and $CXX variables set as well

Finally, if you have your hd5 libraries installed in a non-standard location or the ones in your standard location are old and you want to use newer libraries for whatever reason, you need to edit the CMakeLists.txt file as below


i have added the two lines whereupon make will find the relevant libraries for you if the find function follows

set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} /apps/lab/miket/hdf/1.8.14)
set(CMAKE_INCLUDE_PATH /apps/lab/miket/hdf/1.8.14/include {CMAKE_INCLUDE_PATH})

 how to edit your CMakeLists.txt if you want to include libraries from non-standard location


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