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

Untitled0

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

Untitled1

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

Untitled2

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

Untitled3

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

Untitled5

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

Advertisements