Issue VEP installation MacOS

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14 months ago

Andrea ▴ 10

Hi,

I'm trying to install VEP on Mac. I've tried on the Anaconda Navigator, but I couldn't install. I also tried through the terminal, but also in this way I can't install. The last error that I've got is:

User

cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
#include <lzma.h>

1 error generated.
make: *** [cram/cram_io.o] Error 1
Compile didn't complete. No libhts.a library file found at INSTALL.pl line 881.

Can someone help me?

Thanks!

VEP • 1.1k views

ADD COMMENT • link updated 14 months ago by ATpoint 86k • written 14 months ago by Andrea ▴ 10

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Probably try installing with samtools and htslib added.

ADD REPLY • link 14 months ago by Amitm ★ 2.3k

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I've already installed both samtools and htslib

ADD REPLY • link 14 months ago by Andrea ▴ 10

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you are installing it from within a Makefile? Are you sure that you have the ONESHELL feature active so that your env is propagated between each subsequent Makefile command?

ADD REPLY • link 14 months ago by steve ★ 3.5k

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Ensembl provides a Docker image to run VEP: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html I would go for that. VEP is so lagacy-burden and dependency-heavy that installation from scratch might be a nightmare.

ADD REPLY • link 14 months ago by ATpoint 86k

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