libhts file not found

[Conor Meehan]

Hi,

I am running Platypus built from the latest git clone on an ubuntu machine. I have installed htslib in /usr/local as standard but I am getting the following error:

File "cython/htslibWrapper.pxd", line 203, in init variantcaller (cython/variantcaller.c:17022)

ImportError: libhts.so.1: cannot open shared object file: No such file or directory

When I do a locate libhts.so.1 it is present in /usr/local/lib/

Any idea what is going wrong here?

Thanks in advance,

Conor

[tab...@gmail.com]

I have the exact same problem! It'd be great, if somebody could help us out.

3323

[Daniel Cooke]

I did answer this, but forgot to cc platypus-users...

Hi Daniel,

That worked great, thanks. I don't think that even with /usr/local being used you still have to make these changes in the Makefile is clear on the git page. Might be useful to update this.

thanks again,

Conor

On 24 July 2015 at 14:51, Daniel Cooke <dco...@well.ox.ac.uk> wrote:

Looks like only /lib and /usr/lib paths are standard paths on linux. So you will need to set the path variables documented in the README to /usr/local/{lib, include}.

Best

Dan

On 24 Jul 2015, at 13:29, Conor Meehan <meehan...@gmail.com> wrote:

Hi Daniel,

It is installed in the default directory so I shouldn't need to set the paths according to the Readme file. Am I not understanding that correctly?

Cheers,

Conor

On 24 July 2015 at 14:25, Daniel Cooke <dco...@well.ox.ac.uk> wrote:

Hi Conor,

Probably due to your PATH variables not being set correctly. Please see the README for details on which PATH variables need to be set.

Best

Dan

On 24 Jul 2015, at 13:17, Conor Meehan <meehan...@gmail.com> wrote:

Hi,

I am running Platypus built from the latest git clone on an ubuntu machine. I have installed htslib in /usr/local as standard but I am getting the following error:

File "cython/htslibWrapper.pxd", line 203, in init variantcaller (cython/variantcaller.c:17022)

ImportError: libhts.so.1: cannot open shared object file: No such file or directory

When I do a locate libhts.so.1 it is present in /usr/local/lib/

Any idea what is going wrong here?

Thanks in advance,

Conor

I’ll clarify the README’s at some point.. 

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[Conor Meehan]

So it seems that even if you install htslib in the default directory you still have to link to the location of libhts.so in the Makefile.

Thus you need the 3 lines:

export C_INCLUDE_PATH=/usr/local/include

export LIBRARY_PATH=/usr/local/lib

export LD_LIBRARY_PATH=/usr/local/lib

added to the Makefile of Platypus and that should work.

C

[tab...@gmail.com]

Thank you very much, this solves my problem. 

[Preethi Srinivasan]

where is the Makefile? I don't see one