前提・実現したいこと
バイオインフォマティクス系のソフトウェア(https://sourceforge.net/projects/samtools/files/samtools/0.1.19/)の
インストールを試みたところ、以下のようなエラーが出てしまい、ビルドできません。
解決法をさがしており、なかなかうまいこといかないので、こちらで質問させていただきました。
OSはmacOS High Sierra
です。
$ make make[2]: Nothing to be done for `lib'. make[2]: Nothing to be done for `lib'. make[2]: Nothing to be done for `lib'. gcc -g -Wall -O2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[1]: Nothing to be done for `all'.
INSTALL 注意書き
System Requirements =================== SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA file. SAMtools' faidx is able to index a razip-compressed FASTA file to save diskspace. Older zlib also works with SAMtools, but razip cannot be compiled. The text-based viewer (tview) requires the GNU ncurses library <http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of the modern Linux/Unix distributions. If you do not have this library installed, you can still compile the rest of SAMtools by manually changing: `-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and comment out the line starting with `LIBCURSES='. Compilation =========== Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile razip with `make razip'. Installation ============ Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to a location you want (e.g. a directory in your $PATH). You may also copy `samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such that the `man' command may find the manual.
試したこと
zlib がないのかもと思いましたが、あったようです。
$ brew install zlib Warning: zlib 1.2.11 is already installed and up-to-date To reinstall 1.2.11, run `brew reinstall zlib`
ちなみにファイルの中身です。
/samtools-0.1.19$ ls AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1 bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32 bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
回答3件
あなたの回答
tips
プレビュー
バッドをするには、ログインかつ
こちらの条件を満たす必要があります。
2018/06/24 14:41