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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 Basic Installation
2 ==================
3
4 To build and install HTSlib, 'cd' to the htslib-1.x directory containing
5 the package's source and type the following commands:
6
7 ./configure
8 make
9 make install
10
11 The './configure' command checks your build environment and allows various
12 optional functionality to be enabled (see Configuration below). If you
13 don't want to select any optional functionality, you may wish to omit
14 configure and just type 'make; make install' as for previous versions
15 of HTSlib. However if the build fails you should run './configure' as
16 it can diagnose the common reasons for build failures.
17
18 The 'make' command builds the HTSlib library and and various useful
19 utilities: bgzip, htsfile, and tabix. If compilation fails you should
20 run './configure' as it can diagnose problems with your build environment
21 that cause build failures.
22
23 The 'make install' command installs the libraries, library header files,
24 utilities, several manual pages, and a pkgconfig file to /usr/local.
25 The installation location can be changed by configuring with --prefix=DIR
26 or via 'make prefix=DIR install' (see Installation Locations below).
27
28
29 Configuration
30 =============
31
32 By default, './configure' examines your build environment, checking for
33 requirements such as the zlib development files, and arranges for a plain
34 HTSlib build. The following configure options can be used to enable
35 various features and specify further optional external requirements:
36
37 --with-irods[=DIR]
38 Specifies the location of the iRODS client library to use to enable
39 access to data objects stored in iRODS (<http://irods.org/>) via file
40 paths like 'irods:DATAOBJ'. DIR is the base of an iRODS source tree
41 such that the library is present as DIR/lib/core/obj/libRodsAPI.* and
42 headers are present under DIR/lib/api/include and so on. If '=DIR' is
43 omitted, $IRODS_HOME will be used as a base directory.
44
45 The configure script also accepts the usual options and environment variables
46 for tuning installation locations and compilers: type './configure --help'
47 for details. For example,
48
49 ./configure CC=icc --prefix=/opt/icc-compiled
50
51 would specify that HTSlib is to be built with icc and installed into bin,
52 lib, etc subdirectories under /opt/icc-compiled.
53
54
55 Installation Locations
56 ======================
57
58 By default, 'make install' installs HTSlib libraries under /usr/local/lib,
59 HTSlib header files under /usr/local/include, utility programs under
60 /usr/local/bin, etc. (To be precise, the header files are installed within
61 a fixed 'htslib' subdirectory under the specified .../include location.)
62
63 You can specify a different location to install HTSlib by configuring
64 with --prefix=DIR or specify locations for particular parts of HTSlib by
65 configuring with --libdir=DIR and so on. Type './configure --help' for
66 the full list of such install directory options.
67
68 Alternatively you can specify different locations at install time by
69 typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.
70 Consult the list of prefix/exec_prefix/etc variables near the top of the
71 Makefile for the full list of such variables that can be overridden.
72
73 You can also specify a staging area by typing 'make DESTDIR=DIR install',
74 possibly in conjunction with other --prefix or prefix=DIR settings.
75 For example,
76
77 make DESTDIR=/tmp/staging prefix=/opt
78
79 would install into bin, lib, etc subdirectories under /tmp/staging/opt.