VEP installation can not install Bio::DB:HTS module

xiyasong commented 1 month ago

Describe the issue

A clear and concise description of what the bug is. Hi My VEP installaztion work fine with the --NO_HTSLIB, but when I try to use it for my real sample it gives error: -------------------- EXCEPTION -------------------- MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed

STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:178 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:328 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:94 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::run /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200 STACK toplevel ./vep:46 Date (localtime) = Thu Jul 25 17:49:56 2024 Ensembl API version = 112

So, I tried to install Bio::DB::HTS module, by running perl INSTALL.pl, then it gives error: .... gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread

unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/ ./Bio/tmp/Bio-DB-HTS-2.11 - moving files to ./biodbhts
making Bio::DB:HTS /usr/bin/ld: unrecognized option '-Wl,-O2' /usr/bin/ld: use the --help option for usage information Warning: ExtUtils::CBuilder not installed or no compiler detected Proceeding with configuration, but compilation may fail during Build

Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.11' Building Bio-DB-HTS Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting ERROR: Shared Bio::DB:HTS library not found

Additional information

Please fill in the following sections to help us find the source of your issue as quickly as possible.

System

VEP version: 112
VEP Cache version: 112
Perl version: v5.32.1
OS: Ubuntu
tabix installed ? Yes

Full VEP command line

perl INSTALL.pl

Full error message

Including the warnings, if available Hello! This installer will help you set up VEP v112, including:

Install v112 of the Ensembl API for use by the VEP. It will not affect any existing installations of the Ensembl API that you may have.

Download and install cache files from Ensembl's FTP server.

Download FASTA files from Ensembl's FTP server.

Download VEP plugins.

Checking for installed versions of the Ensembl API...done

Setting up directories

fetching BioPerl
unpacking ./Bio/tmp/release-1-6-924.zip
moving files Attempting to install Bio::DB::HTS and htslib.

If this fails, try re-running with --NO_HTSLIB

checking out HTSLib Cloning into 'htslib'... remote: Enumerating objects: 17111, done. remote: Counting objects: 100% (1388/1388), done. remote: Compressing objects: 100% (668/668), done. remote: Total 17111 (delta 883), reused 916 (delta 687), pack-reused 15723 Receiving objects: 100% (17111/17111), 12.76 MiB | 10.46 MiB/s, done. Resolving deltas: 100% (12292/12292), done. Note: switching to '1832d3a1b75133e55fb6abffc3f50f8a6ed5ceae'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

building HTSLIB in ./htslib In /sza_data/ensembl-vep/htslib echo '/ Default config.h generated by Makefile /' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9-dirty"' > version.h gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hts.o hts.c hts.c: In function ‘hts_idx_init’: hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hts_os.o hts_os.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o md5.o md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o realn.o realn.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o sam.o sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_io.o cram/cram_io.c In file included from /usr/include/string.h:535, from cram/cram_io.c:53: In function ‘strncpy’, inlined from ‘cram_populate_ref’ at cram/cram_io.c:2095:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return _builtinstrncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | glibc_objsize (dest)); | ~~~~~ In function ‘strncpy’, inlined from ‘full_path’ at cram/cram_io.c:3748:13, inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin___strncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | glibc_objsize (dest)); | ~~~~~ In function ‘strncpy’, inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | glibc_objsize (dest)); | ~~~~~ gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o errmod.pico errmod.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hts.pico hts.c hts.c: In function ‘hts_idx_init’: hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hts_os.pico hts_os.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o multipart.pico multipart.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o probaln.pico probaln.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o realn.pico realn.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o textutils.pico textutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c In file included from /usr/include/string.h:535, from cram/cram_io.c:53: In function ‘strncpy’, inlined from ‘cram_populate_ref’ at cram/cram_io.c:2095:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | glibc_objsize (dest)); | ~~~~~ In function ‘strncpy’, inlined from ‘full_path’ at cram/cram_io.c:3748:13, inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | glibc_objsize (dest)); | ~~~~~ In function ‘strncpy’, inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~ gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/hts_endian.o test/hts_endian.c gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/fieldarith.o test/fieldarith.c gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/hfile.o test/hfile.c gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/sam.o test/sam.c gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test_realn.o test/test_realn.c gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test_view.o test/test_view.c gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/ ./Bio/tmp/Bio-DB-HTS-2.11 - moving files to ./biodbhts
making Bio::DB:HTS /usr/bin/ld: unrecognized option '-Wl,-O2' /usr/bin/ld: use the --help option for usage information Warning: ExtUtils::CBuilder not installed or no compiler detected Proceeding with configuration, but compilation may fail during Build

Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.11' Building Bio-DB-HTS Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting ERROR: Shared Bio::DB:HTS library not found

Data files (if applicable)

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jamie-m-a commented 1 month ago

HI @xiyasong

Sorry to hear you've been having trouble with the install. It can be tricky to debug these issues, but there are possibly a couple of simple workarounds.

1) If you run in offline mode, using a cache and fasta file, VEP shouldn't try to use that module, so you can bypass the issue that way. So use --offline, --cache, --dir_cache and --fasta (see here for more details).

2) Failing that, you can try using the containerised docker image of Ensembl VEP - available here, with instructions here. It comes with all dependencies and plugins packaged already.

Do let me know how you get on!

xiyasong commented 1 month ago

Hi, thanks for your kind reply and suggestions, I tried --offline --cache --dir_cache seems still not solved, but luckily: I solved the problem by creating a brand new conda environment and redo everything and it magically works. :)).

Ensembl / ensembl-vep