error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

[qiyubio]

While installing vamos with conda/mamba, there is error while trying to run vamos after make, the error is: "cannot open shared object file: No such file or directory".

ldd vamos is lacking library too. I modified the Makefile accordingly, and now it seems no errors

-PROF=/home1/jingwenr/.conda/envs/trf/lib
+PROF=$(CONDA_PREFIX)/lib
+EXTLIB=-L$(PROF) -Wl,-rpath,$(PROF)

 vamos: main.o io.o vcf.o vntr.o acc_lookup_table.o phase.o msa.o
-       $(CXX) $(CFLAGS) -o $@ $^ -L $(CONDA_PREFIX)/lib $(LIBS) -L ../static_lib/ -lalglib -ledlib -lrt
+       $(CXX) $(CFLAGS) -o $@ $^ $(EXTLIB) $(LIBS) -L ../static_lib/ -lalglib -ledlib -lrt

[mchaisso]

We are working on getting this into conda so that this isn't necessary, if that can't happen soon we'll include this compile.

[maryamghr]

I am facing the same problem, and changing the makefile as recommended by @qiyubio does not work either. Is there any update for this fixing issue?

[mchaisso]

Hi, vamos is now in conda, are you able to install from that?

[maryamghr]

Hi, Thanks for the quick reply. I successfully installed vamos with mamba.

[Hanjunmin]

Hi, Thanks for the quick reply. I successfully installed vamos with mamba.

hi, I meet the same questions, but i also can't install with conda, when I run conda install -c bioconda vamos==1.2.0 thre isn't have this package. and when run conda install -c bioconda vamos, there are many dependencies questions,but i intsall them with thre requirement.txt as reference. Can you help me? Thank you !

[mchaisso]

For now I'm directing people to build from git. I'll try pushing another release to conda now to see if this fixes the issues.

On Wed, Jun 12, 2024 at 9:23 AM Junmin @.***> wrote:

Hi, Thanks for the quick reply. I successfully installed vamos with mamba.

hi, I meet the same questions, but i also can't install with conda, when I run conda install -c bioconda vamos==1.2.0 thre isn't have this package. and when run conda install -c bioconda vamos, there are many dependencies questions,but i intsall them with thre requirement.txt as reference. Can you help me? Thank you !

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