7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/INSTALL src/htslib/INSTALL deleted file mode 100644 index 48602e458cd..00000000000 --- src/htslib/INSTALL +++ /dev/null @@ -1,102 +0,0 @@ -Basic Installation -================== - -To build and install HTSlib, 'cd' to the htslib-1.x directory containing -the package's source and type the following commands: - - ./configure - make - make install - -The './configure' command checks your build environment and allows various -optional functionality to be enabled (see Configuration below). If you -don't want to select any optional functionality, you may wish to omit -configure and just type 'make; make install' as for previous versions -of HTSlib. However if the build fails you should run './configure' as -it can diagnose the common reasons for build failures. - -The 'make' command builds the HTSlib library and and various useful -utilities: bgzip, htsfile, and tabix. If compilation fails you should -run './configure' as it can diagnose problems with your build environment -that cause build failures. - -The 'make install' command installs the libraries, library header files, -utilities, several manual pages, and a pkgconfig file to /usr/local. -The installation location can be changed by configuring with --prefix=DIR -or via 'make prefix=DIR install' (see Installation Locations below). - - -Configuration -============= - -By default, './configure' examines your build environment, checking for -requirements such as the zlib development files, and arranges for a plain -HTSlib build. The following configure options can be used to enable -various features and specify further optional external requirements: - ---enable-plugins - Use plugins to implement exotic file access protocols and other - specialised facilities. This enables such facilities to be developed - and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs - from their library dependencies. By default, any enabled pluggable - facilities (such as iRODS and libcurl file access) are built directly - within HTSlib. - ---with-plugin-dir=DIR - Specifies the directory into which plugins built while building HTSlib - should be installed; by default, LIBEXECDIR/htslib. - ---with-plugin-path=DIR:DIR:DIR... - Specifies the list of directories that HTSlib will search for plugins. - By default, only the directory specified via --with-plugin-dir will be - searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so - on to cause additional directories to be searched. - ---with-irods[=DIR] - Specifies the location of the iRODS client library to use to enable - access to data objects stored in iRODS (<http://irods.org/>) via file - paths like 'irods:DATAOBJ'. DIR is the base of an iRODS source tree - such that the library is present as DIR/lib/core/obj/libRodsAPI.* and - headers are present under DIR/lib/api/include and so on. If '=DIR' is - omitted, $IRODS_HOME will be used as a base directory. - ---enable-libcurl - Use libcurl (<http://curl.haxx.se/>) to implement network access to - remote files via FTP, HTTP, HTTPS, S3, etc. By default, HTSlib uses - its own simple networking code to provide access via FTP and HTTP only. - -The configure script also accepts the usual options and environment variables -for tuning installation locations and compilers: type './configure --help' -for details. For example, - - ./configure CC=icc --prefix=/opt/icc-compiled - -would specify that HTSlib is to be built with icc and installed into bin, -lib, etc subdirectories under /opt/icc-compiled. - - -Installation Locations -====================== - -By default, 'make install' installs HTSlib libraries under /usr/local/lib, -HTSlib header files under /usr/local/include, utility programs under -/usr/local/bin, etc. (To be precise, the header files are installed within -a fixed 'htslib' subdirectory under the specified .../include location.) - -You can specify a different location to install HTSlib by configuring -with --prefix=DIR or specify locations for particular parts of HTSlib by -configuring with --libdir=DIR and so on. Type './configure --help' for -the full list of such install directory options. - -Alternatively you can specify different locations at install time by -typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on. -Consult the list of prefix/exec_prefix/etc variables near the top of the -Makefile for the full list of such variables that can be overridden. - -You can also specify a staging area by typing 'make DESTDIR=DIR install', -possibly in conjunction with other --prefix or prefix=DIR settings. -For example, - - make DESTDIR=/tmp/staging prefix=/opt - -would install into bin, lib, etc subdirectories under /tmp/staging/opt.