HISAT2 compilation error: cannot find various static files

Question

[limsingwei2]

Hi I'm a newbie to bioinformatics, and I was trying to compile Hisat2 from source code to enable the sra-acc function for Hisat to directly extract files from SRA. To build from the source code I inputed:

make USE_SRA=1 NCBI_NGS_DIR=/home/lsw2003/softwares/ncbi/ngs NCBI_VDB_DIR=/home/lsw2003/softwares/ncbi/ncbi-vdb

but it was unable to compile, error message gave me this:

/usr/bin/ld: cannot find -lncbi-ngs-c++-static
/usr/bin/ld: cannot find -lngs-c++-static
/usr/bin/ld: cannot find -lncbi-vdb-static
collect2: error: ld returned 1 exit status
make: *** [Makefile:382: hisat2-align-s] Error 1

and I can't seem to find any help for this error Any guidance much appreciated!

[ATpoint]

Why do you need to compile, there are precompiled binaries for the Linux and Mac plus you can install it via package managers such as conda and homebrew. Make your life easy and use any of those options.

[limsingwei2]

Thank you very much for your answer! I did try the precompiled verions (namely conda) but the sra-acc function didnt seem to work on those...and the hisat2 manual seems to imply that I have to change the variables for make to get SRA access: "For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit. When running make, specify additional variables as follow. make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options. For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used."