質問編集履歴
3
zlib install
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make[1]: Nothing to be done for `all'.
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```
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ちなみにファイルの中身です。
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```
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/samtools-0.1.19$ ls
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AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
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COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
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ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
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INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
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Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
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Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
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NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
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bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
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bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
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bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
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bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
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bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
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bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
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bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
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INSTALL 注意書き
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```
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-
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INSTALL の中身
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```
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System Requirements
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===================
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a location you want (e.g. a directory in your $PATH). You may also copy
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`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
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that the `man' command may find the manual.
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```
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### 試したこと
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zlib がないのかもと思いましたが、あったようです。
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```
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$ brew install zlib
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Warning: zlib 1.2.11 is already installed and up-to-date
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To reinstall 1.2.11, run `brew reinstall zlib`
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```
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###
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ちなみにファイルの中身です。
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```
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/samtools-0.1.19$ ls
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65
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AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
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66
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COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
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ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
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INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
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Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
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Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
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NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
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bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
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bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
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bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
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bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
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bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
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bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
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bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
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```
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2
INSTALL の注意書き追加
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File without changes
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body
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@@ -33,4 +33,38 @@
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bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
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bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
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```
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INSTALL の中身
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```
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System Requirements
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===================
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SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
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preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
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file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
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diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
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The text-based viewer (tview) requires the GNU ncurses library
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<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
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the modern Linux/Unix distributions. If you do not have this library installed,
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you can still compile the rest of SAMtools by manually changing:
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`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
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comment out the line starting with `LIBCURSES='.
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Compilation
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===========
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Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
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razip with `make razip'.
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Installation
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============
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Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
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a location you want (e.g. a directory in your $PATH). You may also copy
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68
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`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
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69
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that the `man' command may find the manual.
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```
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1
OS名
title
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File without changes
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body
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@@ -3,6 +3,7 @@
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3
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バイオインフォマティクス系のソフトウェア（https://sourceforge.net/projects/samtools/files/samtools/0.1.19/）の
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インストールを試みたところ、以下のようなエラーが出てしまい、ビルドできません。
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解決法をさがしており、なかなかうまいこといかないので、こちらで質問させていただきました。
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OSは`macOS High Sierra`です。
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```
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$ make
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@@ -13,4 +14,23 @@
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gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
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make[1]: Nothing to be done for `all'.
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15
16
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17
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```
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18
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+
ちなみにファイルの中身です。
|
|
19
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+
```
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20
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+
/samtools-0.1.19$ ls
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21
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+
AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
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22
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+
COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
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23
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+
ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
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24
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+
INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
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25
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+
Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
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26
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+
Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
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27
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+
NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
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28
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+
bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
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29
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bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
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30
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+
bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
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31
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bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
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bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
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33
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+
bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
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34
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+
bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
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35
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+
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16
36
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```
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