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Fixes for the build system. Rename jellyfish binaries to avoid name clases on systems that already include jellyfish.
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@@ -25,21 +25,25 @@ Generic installation description can be found in the INSTALL file. Short summary | |
| - Acquire the source code. Either download and decompress the distributable ("tar -xvf kat-<version>.tar.gz"), or clone the git repository (For ssh: ```git clone [email protected]:TGAC/KAT.git```; or for https: ```git clone https://github.com/TGAC/KAT.git```), into a directory on your machine. | ||
| - "cd" into root directory of the installation | ||
| - Ensure these tools are correctly installed and available on your system: | ||
| - gcc tool chain | ||
| - gcc V4.9+ | ||
| - autoconf V2.53+ | ||
| - automake V1.11+ | ||
| - libtool V2.4.2+ | ||
| - make | ||
| - boost V1.53+ | ||
| - gnuplot (required for plotting at runtime, must be available on the path to use this functionality) - http://www.gnuplot.info | ||
| - If you cloned the git repository you must first run "./autogen.sh" to create the configure and make files for your project. (If you downloaded a source code distribution tarball then you can skip this step.) | ||
| - For a typical installation on a machine where you have root access type ```./configure; make; sudo make install;``` | ||
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| The configure script can take several options as arguments. One commonly modified option is ```--prefix```, which will install KAT to a custom directory. By default this is "/usr/local", so the KAT executable would be found at "/usr/local/bin" by default. In addition, some options specific to managing KAT dependencies located in non-standard locations are: | ||
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| - ```--with-boost``` - for specifying a custom boost directory (boost is only required for unit testing) | ||
| - ```--with-boost``` - for specifying a custom boost directory | ||
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| Type ```./configure --help``` for full details. | ||
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| The Makefile for KAT can take several goals. Full details of common make goals can be found in the INSTALL file. Typically, the following options can optionally used by KAT: | ||
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| - ```make check``` - runs unit tests. *NOTE*: Requires boost unit test framework to be installed and available. | ||
| - ```make check``` - runs unit tests. | ||
| - ```make dist``` - packages the installation into a tarballed distributable. | ||
| - ```make distcheck``` - runs some sanity tests to ensure the tarballed distributable is likely to work. | ||
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@@ -3,7 +3,7 @@ | |
| ########################################################################## | ||
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| # Autoconf initialistion. Sets package name version and contact details | ||
| AC_INIT([Kmer Analysis Toolkit (KAT)],[2.0.7],[[email protected] and/or [email protected]],[kat],[http://www.tgac.ac.uk/kat]) | ||
| AC_INIT([Kmer Analysis Toolkit (KAT)],[2.0.8],[[email protected] and/or [email protected]],[kat],[http://www.tgac.ac.uk/kat]) | ||
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| # Require autoconf 2.53 or higher | ||
| AC_PREREQ([2.53]) | ||
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@@ -111,6 +111,6 @@ AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_STATIC_LIBS}" | |
| AC_SUBST([AM_LIBS]) | ||
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| AC_CONFIG_HEADERS([config.h]) | ||
| AC_CONFIG_FILES([Makefile src/Makefile tests/Makefile]) | ||
| AC_CONFIG_FILES([Makefile src/Makefile tests/Makefile deps/seqan-library-2.0.0/Makefile]) | ||
| AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0]) | ||
| AC_OUTPUT | ||
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| @@ -0,0 +1 @@ | ||
| *.txt |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,4 @@ | ||
| AC_INIT([jellyfish], [2.2.0], [[email protected]]) | ||
| AC_INIT([jellyfish], [k2.2.0], [[email protected]]) | ||
| AC_CANONICAL_HOST | ||
| AC_CONFIG_MACRO_DIR([m4]) | ||
| AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests]) | ||
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@@ -14,7 +14,7 @@ AC_LANG(C++) | |
| AC_PROG_CXX | ||
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| # Major version of the library | ||
| AC_SUBST([PACKAGE_LIB], [2.0]) | ||
| AC_SUBST([PACKAGE_LIB], [k2.0]) | ||
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| # Check for md5 or md5sum | ||
| AC_ARG_VAR([MD5], [Path to md5 hashing program]) | ||
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@@ -27,7 +27,7 @@ AC_ARG_VAR([YAGGO], [Yaggo switch parser generator]) | |
| AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])]) | ||
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| dnl define([concat], $1$2$3)dnl | ||
| define([PC_FILE], jellyfish-2.0.pc) | ||
| define([PC_FILE], jellyfish-k2.0.pc) | ||
| AC_CONFIG_FILES([ | ||
| Makefile | ||
| tests/compat.sh | ||
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| @@ -0,0 +1 @@ | ||
| /Makefile |
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