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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Using a non-bundled htslib version #331

Closed samfux84 closed 4 years ago

samfux84 commented 4 years ago

Hi,

Is it possible to use a non-bundled htslib to build lumpy-sv 0.3.0 ?

Because using the bundled one requires to clone with "git clone --recursive", which makes the releases provided in https://github.com/arq5x/lumpy-sv/releases useless as they don't contain the content of the htslib directory.

We have several htslib versions installed on our cluster, and I prefer to build from a release tarball instead of using git clone --recursive.

Best regards

Sam

samfux84 commented 4 years ago

Will removing

htslib:
        $(shell cd lib/htslib && autoreconf)
        cd lib/htslib && \
        ./configure --disable-bz2 --disable-lzma --enable-libcurl
        CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT"

from the Makefile and providing an external htslib break lumpy-sv ?

ryanlayer commented 4 years ago

You can also just remove the "htslib" from the "lumpy_filter: htslib" line

After that you need to edit lumpy-sv/src/filter/Makefile to point at the htslib you want

On Fri, Mar 27, 2020 at 5:41 AM Samuel Fux notifications@github.com wrote:

Will removing

htslib: $(shell cd lib/htslib && autoreconf) cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT"

from the Makefile and providing an external htslib break lumpy-sv ?

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samfux84 commented 4 years ago

@ryanlayer: Thank you very much for your reply.

I tried building version 0.3.0 with the SPACK package manager that so far only supports version 0.2.13:

https://spack.readthedocs.io/en/latest/package_list.html#lumpy-sv

I could not manage to adapt the package such that it also builds version 0.3.0 fine, therefore I just installed it manually, following your documentation with git clone --recursive.

In any case thank you for being responsive and for providing help.

Best regards

Sam

ryanlayer commented 4 years ago

Sorry that first idea didnt work, but now that you have things built please use smoove to run lumpy

https://github.com/brentp/smoove

On Fri, Mar 27, 2020 at 6:53 AM Samuel Fux notifications@github.com wrote:

@ryanlayer https://github.com/ryanlayer: Thank you very much for your reply.

I tried building version 0.3.0 with the SPACK package manager that so far only supports version 0.2.13:

https://spack.readthedocs.io/en/latest/package_list.html#lumpy-sv

I could not manage to adapt the package such that it also builds version 0.3.0 fine, therefore I just installed it manually, following your documentation with git clone --recursive.

In any case thank you for being responsive and for providing help.

Best regards

Sam

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/arq5x/lumpy-sv/issues/331#issuecomment-604984028, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEUGULA7NLRLW7IKYKS763RJSOTRANCNFSM4LU5YCEQ .