samtools 설치하기

안녕하세요

한주현입니다

오늘은 samtools 설치에 대하여 알아보겠습니다

참조 URL

http://www.htslib.org/doc/samtools.html

http://www.htslib.org/download/

다음 URL에 들어가시거나

http://www.htslib.org/download/

또는 제가 아래에 준비한 링크를 직접 받으셔도 됩니다

다운로드 링크

https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2

이제 본격적으로 설치해보죠..

1) 압축해제

$ tar xf samtools-1.3.1.tar.bz2

2) 설치

$ make

$ make prefix=경로지정 install

설치과정

Makefile:98: config.mk: No such file or directory
echo '/* Basic config.h generated by Makefile */' > config.h
echo '#define HAVE_CURSES' >> config.h
echo '#define HAVE_CURSES_H' >> config.h
gcc -g -Wall -O2 -I. -Ihtslib-1.3.1  -c -o bam_index.o bam_index.c
gcc -g -Wall -O2 -I. -Ihtslib-1.3.1  -c -o bam_plcmd.o bam_plcmd.c
gcc -g -Wall -O2 -I. -Ihtslib-1.3.1  -c -o sam_view.o sam_view.c
...

<생략>

...

mkdir -p -m 755 /home/jhan/etc/samtools-1.3.1/bin /home/jhan/etc/samtools-1.3.1/share/man/man1
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /home/jhan/etc/samtools-1.3.1/bin
install -p -m 644 samtools.1 misc/wgsim.1 /home/jhan/etc/samtools-1.3.1/share/man/man1

확인

$ pwd

/home/jhan/etc/samtools-1.3.1/bin

$ ls -l

total 4440
drwxr-xr-x 2 jhan jhan    4096  3월 14 12:24 ./
drwxrwxr-x 4 jhan jhan    4096  3월 14 12:24 ../
-rwxr-xr-x 1 jhan jhan   76095  3월 14 12:24 ace2sam*
-rwxr-xr-x 1 jhan jhan    5328  8월 19  2014 blast2sam.pl*
-rwxr-xr-x 1 jhan jhan    3364  8월 19  2014 bowtie2sam.pl*
-rwxr-xr-x 1 jhan jhan   18032  8월  1  2014 export2sam.pl*
-rwxr-xr-x 1 jhan jhan    6125  8월 19  2014 interpolate_sam.pl*
-rwxr-xr-x 1 jhan jhan   25464  3월 14 12:24 maq2sam-long*
-rwxr-xr-x 1 jhan jhan   25456  3월 14 12:24 maq2sam-short*
-rwxr-xr-x 1 jhan jhan   39811  3월 14 12:24 md5fa*
-rwxr-xr-x 1 jhan jhan   29251  3월 14 12:24 md5sum-lite*
-rwxr-xr-x 1 jhan jhan    6773  9월  2  2014 novo2sam.pl*
-rwxr-xr-x 1 jhan jhan   48367  5월 28  2015 plot-bamstats*
-rwxr-xr-x 1 jhan jhan    3208  8월 19  2014 psl2sam.pl*
-rwxr-xr-x 1 jhan jhan    8961  8월 19  2014 sam2vcf.pl*
-rwxr-xr-x 1 jhan jhan 4083677  3월 14 12:24 samtools*
-rwxr-xr-x 1 jhan jhan   16478  8월 19  2014 samtools.pl*
-rwxr-xr-x 1 jhan jhan   11105  1월 28  2015 seq_cache_populate.pl*
-rwxr-xr-x 1 jhan jhan    3909  8월 19  2014 soap2sam.pl*
-rwxr-xr-x 1 jhan jhan    7888  8월 19  2014 varfilter.py*
-rwxr-xr-x 1 jhan jhan   61729  3월 14 12:24 wgsim*
-rwxr-xr-x 1 jhan jhan   12540 10월 15  2014 wgsim_eval.pl*
-rwxr-xr-x 1 jhan jhan    3583  8월 19  2014 zoom2sam.pl*
$

완료

$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.3.1 (using htslib 1.3.1)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     rmdup          remove PCR duplicates
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

이상으로 samtools 설치에 대하여 알아보았습니다

그럼 다음에 봐요~