Issue VEP installation MacOS
0
0
Entering edit mode
13 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 • 1.0k views
ADD COMMENT
1
Entering edit mode

Probably try installing with samtools and htslib added.

ADD REPLY
0
Entering edit mode

I've already installed both samtools and htslib

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 1896 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6