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vymao opened this issue May 22, 2020 · 1 comment
Open

HTSlib installed but not found? #2

vymao opened this issue May 22, 2020 · 1 comment

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@vymao
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vymao commented May 22, 2020

I have tried running ./build.sh with HTSlib as a loaded module (on a cluster) and built from source; however, both times I get the same message:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for gengetopt... yes
checking for bam_endpos in -lhts... no
configure: error: please install htslib

Would you know how to fix this?

@sid-code
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sid-code commented May 22, 2020

Can you paste the contents of the htslib modulefile? I suspect it's not setting the LD_LIBRARY_PATH or LIBRARY_PATH variables correctly, or something like that. I'm testing it on my local machine with htslib version 1.10.2 and the configure script finds it just fine.

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