質問編集履歴
3
zlib install
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -32,47 +32,9 @@
|
|
|
32
32
|
|
|
33
33
|
```
|
|
34
34
|
|
|
35
|
-
ちなみにファイルの中身です。
|
|
36
|
-
|
|
37
|
-
```
|
|
38
|
-
|
|
39
|
-
/samtools-0.1.19$ ls
|
|
40
|
-
|
|
41
|
-
AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
|
|
42
|
-
|
|
43
|
-
COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
|
|
44
|
-
|
|
45
|
-
ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
|
|
46
|
-
|
|
47
|
-
INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
|
|
48
|
-
|
|
49
|
-
Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
|
|
50
|
-
|
|
51
|
-
Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
|
|
52
|
-
|
|
53
|
-
NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
|
|
54
|
-
|
|
55
|
-
bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
|
|
56
|
-
|
|
57
|
-
bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
|
|
58
|
-
|
|
59
|
-
bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
|
|
60
|
-
|
|
61
|
-
bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
|
|
62
|
-
|
|
63
|
-
bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
|
|
64
|
-
|
|
65
|
-
bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
|
|
66
|
-
|
|
67
|
-
bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
|
|
68
35
|
|
|
69
36
|
|
|
70
|
-
|
|
71
|
-
```
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
INSTALL
|
|
37
|
+
INSTALL 注意書き
|
|
76
38
|
|
|
77
39
|
```
|
|
78
40
|
|
|
@@ -137,3 +99,61 @@
|
|
|
137
99
|
that the `man' command may find the manual.
|
|
138
100
|
|
|
139
101
|
```
|
|
102
|
+
|
|
103
|
+
|
|
104
|
+
|
|
105
|
+
### 試したこと
|
|
106
|
+
|
|
107
|
+
zlib がないのかもと思いましたが、あったようです。
|
|
108
|
+
|
|
109
|
+
```
|
|
110
|
+
|
|
111
|
+
$ brew install zlib
|
|
112
|
+
|
|
113
|
+
Warning: zlib 1.2.11 is already installed and up-to-date
|
|
114
|
+
|
|
115
|
+
To reinstall 1.2.11, run `brew reinstall zlib`
|
|
116
|
+
|
|
117
|
+
```
|
|
118
|
+
|
|
119
|
+
|
|
120
|
+
|
|
121
|
+
###
|
|
122
|
+
|
|
123
|
+
ちなみにファイルの中身です。
|
|
124
|
+
|
|
125
|
+
```
|
|
126
|
+
|
|
127
|
+
/samtools-0.1.19$ ls
|
|
128
|
+
|
|
129
|
+
AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
|
|
130
|
+
|
|
131
|
+
COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
|
|
132
|
+
|
|
133
|
+
ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
|
|
134
|
+
|
|
135
|
+
INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
|
|
136
|
+
|
|
137
|
+
Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
|
|
138
|
+
|
|
139
|
+
Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
|
|
140
|
+
|
|
141
|
+
NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
|
|
142
|
+
|
|
143
|
+
bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
|
|
144
|
+
|
|
145
|
+
bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
|
|
146
|
+
|
|
147
|
+
bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
|
|
148
|
+
|
|
149
|
+
bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
|
|
150
|
+
|
|
151
|
+
bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
|
|
152
|
+
|
|
153
|
+
bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
|
|
154
|
+
|
|
155
|
+
bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
|
|
156
|
+
|
|
157
|
+
|
|
158
|
+
|
|
159
|
+
```
|
2
INSTALL の注意書き追加
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -69,3 +69,71 @@
|
|
|
69
69
|
|
|
70
70
|
|
|
71
71
|
```
|
|
72
|
+
|
|
73
|
+
|
|
74
|
+
|
|
75
|
+
INSTALL の中身
|
|
76
|
+
|
|
77
|
+
```
|
|
78
|
+
|
|
79
|
+
System Requirements
|
|
80
|
+
|
|
81
|
+
===================
|
|
82
|
+
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
|
|
86
|
+
|
|
87
|
+
preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
|
|
88
|
+
|
|
89
|
+
file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
|
|
90
|
+
|
|
91
|
+
diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
|
|
92
|
+
|
|
93
|
+
|
|
94
|
+
|
|
95
|
+
The text-based viewer (tview) requires the GNU ncurses library
|
|
96
|
+
|
|
97
|
+
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
|
|
98
|
+
|
|
99
|
+
the modern Linux/Unix distributions. If you do not have this library installed,
|
|
100
|
+
|
|
101
|
+
you can still compile the rest of SAMtools by manually changing:
|
|
102
|
+
|
|
103
|
+
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
|
|
104
|
+
|
|
105
|
+
comment out the line starting with `LIBCURSES='.
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
|
|
110
|
+
|
|
111
|
+
Compilation
|
|
112
|
+
|
|
113
|
+
===========
|
|
114
|
+
|
|
115
|
+
|
|
116
|
+
|
|
117
|
+
Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
|
|
118
|
+
|
|
119
|
+
razip with `make razip'.
|
|
120
|
+
|
|
121
|
+
|
|
122
|
+
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
Installation
|
|
126
|
+
|
|
127
|
+
============
|
|
128
|
+
|
|
129
|
+
|
|
130
|
+
|
|
131
|
+
Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
|
|
132
|
+
|
|
133
|
+
a location you want (e.g. a directory in your $PATH). You may also copy
|
|
134
|
+
|
|
135
|
+
`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
|
|
136
|
+
|
|
137
|
+
that the `man' command may find the manual.
|
|
138
|
+
|
|
139
|
+
```
|
1
OS名
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -7,6 +7,8 @@
|
|
|
7
7
|
インストールを試みたところ、以下のようなエラーが出てしまい、ビルドできません。
|
|
8
8
|
|
|
9
9
|
解決法をさがしており、なかなかうまいこといかないので、こちらで質問させていただきました。
|
|
10
|
+
|
|
11
|
+
OSは`macOS High Sierra`です。
|
|
10
12
|
|
|
11
13
|
|
|
12
14
|
|
|
@@ -29,3 +31,41 @@
|
|
|
29
31
|
|
|
30
32
|
|
|
31
33
|
```
|
|
34
|
+
|
|
35
|
+
ちなみにファイルの中身です。
|
|
36
|
+
|
|
37
|
+
```
|
|
38
|
+
|
|
39
|
+
/samtools-0.1.19$ ls
|
|
40
|
+
|
|
41
|
+
AUTHORS bam2bcf_indel.c bam_index.o bam_rmdup.o bamshuf.c cut_target.o knetfile.h phase.c sam_view.c
|
|
42
|
+
|
|
43
|
+
COPYING bam2bcf_indel.o bam_lpileup.c bam_rmdupse.c bamshuf.o errmod.c knetfile.o phase.o sam_view.o
|
|
44
|
+
|
|
45
|
+
ChangeLog.old bam2depth.c bam_lpileup.o bam_rmdupse.o bamtk.c errmod.h kprobaln.c razf.c sample.c
|
|
46
|
+
|
|
47
|
+
INSTALL bam2depth.o bam_mate.c bam_sort.c bamtk.o errmod.o kprobaln.h razf.h sample.h
|
|
48
|
+
|
|
49
|
+
Makefile bam_aux.c bam_mate.o bam_sort.o bcftools examples kprobaln.o razf.o sample.o
|
|
50
|
+
|
|
51
|
+
Makefile.mingw bam_aux.o bam_md.c bam_stat.c bedcov.c faidx.c kseq.h razip samtools
|
|
52
|
+
|
|
53
|
+
NEWS bam_cat.c bam_md.o bam_stat.o bedcov.o faidx.h ksort.h razip.c samtools.1
|
|
54
|
+
|
|
55
|
+
bam.c bam_cat.o bam_pileup.c bam_tview.c bedidx.c faidx.o kstring.c razip.o win32
|
|
56
|
+
|
|
57
|
+
bam.h bam_color.c bam_pileup.o bam_tview.h bedidx.o kaln.c kstring.h sam.c
|
|
58
|
+
|
|
59
|
+
bam.h~ bam_color.o bam_plcmd.c bam_tview.o bgzf.c kaln.h kstring.o sam.h
|
|
60
|
+
|
|
61
|
+
bam.o bam_endian.h bam_plcmd.o bam_tview_curses.c bgzf.h kaln.o libbam.a sam.o
|
|
62
|
+
|
|
63
|
+
bam2bcf.c bam_import.c bam_reheader.c bam_tview_curses.o bgzf.o khash.h misc sam_header.c
|
|
64
|
+
|
|
65
|
+
bam2bcf.h bam_import.o bam_reheader.o bam_tview_html.c bgzip.c klist.h padding.c sam_header.h
|
|
66
|
+
|
|
67
|
+
bam2bcf.o bam_index.c bam_rmdup.c bam_tview_html.o cut_target.c knetfile.c padding.o sam_header.o
|
|
68
|
+
|
|
69
|
+
|
|
70
|
+
|
|
71
|
+
```
|