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SNPs were initially characterized by their unique occurrence in several groups of G.
#Install samtools on mac how to
I am wondering how to overcome the issue. Install samtools: sudo apt-get -y install samtools. Make: *** Error 1 Describe the solution you would like.Īs other suggested in other discussion stream for Bio::DB::HTS module, I edited the makefile to add -fPIC to CFLAGS but it still didn't work. Ld: symbol(s) not found for architecture x86_64Ĭlang: error: linker command failed with exit code 1 (use -v to see invocation) _ks_introsort_heap in libbam.a(bam_sort.o) Samtools is a suite of programs for interacting with high-throughput sequencing data. _ks_combsort_heap in libbam.a(bam_sort.o) Undefined symbols for architecture x86_64: Gcc -g -Wall -O2 -fPIC -m64 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz Explanation of the values returned by the application: Returned value. Gcc -c -g -Wall -O2 -fPIC -m64 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. Samtools flags is a simple tool that returns the value or values of a flag that you can find in SAM,BAM and CRAM files.
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While I am trying to install it via Shell, it returns the error message at last: As indicated in the README file from Bio::DB::Sam, it only works with samtools up to version 0.1.17.
#Install samtools on mac update
conda macOS 10.14 Mojave : Operation not permitted when executing conda update -all. I need to install the Bio::DB::Sam for the HTGTS pipeline (. Next install htslib to access the command line functionality of Samtools. conda install -c bioconda samtools1.9h8ee4bcc1 openssl1.0.