From c1813641634f9021f61ba0585ebbbc63cc644797 Mon Sep 17 00:00:00 2001 From: gmarcais Date: Wed, 8 Apr 2015 09:05:57 -0400 Subject: [PATCH 1/3] Update README.md --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 33fb4995..8c8af708 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ If you use Jellyfish in your research, please cite: Installation ------------ -To get an easier to compiled packaged tar ball of the source code, see the [home page of Jellyfish at the University of Maryland][1]. +To get an easier to compiled packaged tar ball of the source code, download a release from [home page of Jellyfish at the University of Maryland][1] or from the [github release][3]. To compile from the git tree, you will need autoconf/automake, make, g++ 4.4 or newer and [yaggo](https://github.com/gmarcais/yaggo "Yaggo on github"). Then compile with: @@ -35,15 +35,15 @@ In the examples directory are potentially useful extra programs to query/manipul Binding to script languages --------------------------- -Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the tarball provided on [Jellyfish's home page][1]. +Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the [release tarball][3]: [SWIG][2] is not required and in the command lines shown below, remove the `--enable-swig` switch. Only the development files of the scripting languages are required. -Compilation of the bindings from the git tree requires [SWIG](http://swig.org) version 3, and the development files of the scripting languages. To compile all three bindings, configure with: +Compilation of the bindings from the git tree requires [SWIG][2] version 3, and the development files of the scripting languages. To compile all three bindings, configure with: ```Shell ./configure --enable-swig --enable-ruby-binding --enable-python-binding --enable-perl-binding ``` -Note that the headers of older version of Perl 5 do not compile with recent compilers (g++ > 4.4, clang++) and C++11 mode enable. One may have to specify in addition `CXX=g++4.4` to compile the perl binding. +Note that the headers of older version of Perl 5 do not compile with recent compilers (g++ > 4.4, clang++) and C++11 mode enable. One may have to specify the path to version 4.4 of gcc by adding, for example, `CXX=g++4.4` to the configure commande line. The binding can installed in a different location than the default (which may require root privileges for example) by passing a path to the `--enable` switches. Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted (`PYTHONPATH`, `RUBYLIB` and `PERL5LIB` respectively). For example: @@ -55,3 +55,5 @@ export PYTHONPATH=$HOME/lib/python See the `swig` directory for examples on how to use the bindings. [1]: http://www.genome.umd.edu/jellyfish.html "Genome group at University of Maryland" +[2]: http://www.swig.org/ +[3]: https://github.com/gmarcais/Jellyfish/releases "Jellyfish release" From c1f4e1433995ac3e0e96d13dfa0c7e795bd9ca14 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 24 Jun 2015 17:04:06 +1000 Subject: [PATCH 2/3] use $(SHELL) in Makefile instead of hard coding /bin/sh for systems where /bin/sh does not exist. --- Makefile.am | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile.am b/Makefile.am index 40c37409..7fb628b0 100644 --- a/Makefile.am +++ b/Makefile.am @@ -136,7 +136,7 @@ YAGGO_SOURCES += jellyfish/generate_sequence_cmdline.hpp # Tests # ######### TEST_EXTENSIONS = .sh -SH_LOG_COMPILER = /bin/sh +SH_LOG_COMPILER = $(SHELL) AM_SH_LOG_FLAGS = TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh \ From fcd341859d98af036ac69419f13c223bcfeb0055 Mon Sep 17 00:00:00 2001 From: Guillaume Marcais Date: Wed, 24 Jun 2015 12:19:09 -0400 Subject: [PATCH 3/3] Bumped version to 2.2.2 --- configure.ac | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.ac b/configure.ac index 9c6a865b..623e6c3b 100644 --- a/configure.ac +++ b/configure.ac @@ -1,4 +1,4 @@ -AC_INIT([jellyfish], [2.2.1], [gmarcais@umd.edu]) +AC_INIT([jellyfish], [2.2.2], [gmarcais@umd.edu]) AC_CANONICAL_HOST AC_CONFIG_MACRO_DIR([m4]) AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])