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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Problem finding "htslib_static.mk" on make #105

Closed dnbuckley closed 3 years ago

dnbuckley commented 3 years ago

I get the following error when I try to make after configuring:

Making all in src/cdflib90 make[1]: Entering directory/home1/dnbuckle/bin/lofreq/src/cdflib90' make[1]: Nothing to be done for all'. make[1]: Leaving directory/home1/dnbuckle/bin/lofreq/src/cdflib90' Making all in src/uthash make[1]: Entering directory /home1/dnbuckle/bin/lofreq/src/uthash' make[1]: Nothing to be done forall'. make[1]: Leaving directory /home1/dnbuckle/bin/lofreq/src/uthash' Making all in src/lofreq make[1]: Entering directory/home1/dnbuckle/bin/lofreq/src/lofreq' Makefile:642: /home1/dnbuckle/bin/lib/htslib-1.10.2//htslib_static.mk: No such file or directory make[1]: No rule to make target /home1/dnbuckle/bin/lib/htslib-1.10.2//htslib_static.mk'. Stop. make[1]: Leaving directory/home1/dnbuckle/bin/lofreq/src/lofreq' make: [all-recursive] Error 1`

I've looked for "htslib_static.mk" everywhere I can think of, I've tried rebuilding my htslib, I've tried prayer, nothing seems to fix it.

Thanks in advance for advance for any help, DB

andreas-wilm commented 3 years ago

Hi David,

Apologies for the late reply. I have to admit the error message doesn't intuitively make sense to me either. Could you post the full sequence of commands (even before ./configure etc/) please?

Many thanks, Andreas

On Thu, 12 Nov 2020 at 07:14, David Buckley notifications@github.com wrote:

I get the following error when I try to make after configuring:

Making all in src/cdflib90 make[1]: Entering directory /home1/dnbuckle/bin/lofreq/src/cdflib90' make[1]: Nothing to be done for all'. make[1]: Leaving directory /home1/dnbuckle/bin/lofreq/src/cdflib90' Making all in src/uthash make[1]: Entering directory /home1/dnbuckle/bin/lofreq/src/uthash' make[1]: Nothing to be done for all'. make[1]: Leaving directory /home1/dnbuckle/bin/lofreq/src/uthash' Making all in src/lofreq make[1]: Entering directory /home1/dnbuckle/bin/lofreq/src/lofreq' Makefile:642: /home1/dnbuckle/bin/lib/htslib-1.10.2//htslib_static.mk: No such file or directory make[1]: No rule to make target /home1/dnbuckle/bin/lib/htslib-1.10.2//htslib_static.mk'. Stop. make[1]: Leaving directory /home1/dnbuckle/bin/lofreq/src/lofreq' make: [all-recursive] Error 1`

I've looked for "htslib_static.mk" everywhere I can think of, I've tried rebuilding my htslib, I've tried prayer, nothing seems to fix it.

Thanks in advance for advance for any help, DB

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-- Andreas Wilm andreas.wilm@gmail.com | 0x7C68FBCC

joanmarticarreras commented 3 years ago

Hi @dnbuckley ,

I faced a similar problem. When running make an error was raised that htslib_static.mk could not be found. It was solved by entering the absolute path to my HTS library at ./configure --with-htslib= instead of a relative path.

I hope it helps.

Warm regards,

Joan

andreas-wilm commented 3 years ago

Hope it's okay to close