diff --git a/AUTHORS b/AUTHORS index ab74a791..08c148a7 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,3 +1,4 @@ -Daniel Mapleson -Luca Venturini -David Swarbreck +Daniel Mapleson +David Swarbreck +Luca Venturini + diff --git a/configure.ac b/configure.ac index 1c066212..8cf1b6c0 100644 --- a/configure.ac +++ b/configure.ac @@ -4,7 +4,7 @@ # Autoconf setup AC_PREREQ([2.68]) -AC_INIT([portcullis],[0.17.2],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk]) +AC_INIT([portcullis],[0.17.3],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk]) AC_CONFIG_SRCDIR([src/portcullis.cc]) AC_CONFIG_AUX_DIR([build-aux]) AC_CONFIG_MACRO_DIR([m4]) diff --git a/doc/source/conf.py b/doc/source/conf.py index eb3ee399..04808998 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -53,9 +53,9 @@ # built documents. # # The short X.Y version. -version = '0.17.2' +version = '0.17.3' # The full version, including alpha/beta/rc tags. -release = '0.17.2' +release = '0.17.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/doc/source/installation.rst b/doc/source/installation.rst index 148aae05..6dcc6f7b 100644 --- a/doc/source/installation.rst +++ b/doc/source/installation.rst @@ -4,14 +4,14 @@ Installation ============ Portcullis is primarily a C++ application with some python scripts. We use the -GNU build system ``Autotools`` to assist with package management and to make the +GNU build system *Autotools* to assist with package management and to make the software portable across UNIX type operating systems. Installation of portcullis therefore follows a similar incantation to other autotools based projects:: - ```./configure; make; sudo make install;``` + ./configure && make && sudo make install However, there are a few caveats. If you cloned the software directly from the -git repository you must first run "./autogen.sh" to create the configure and make +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 those scripts are already present so you can skip this step. @@ -32,20 +32,20 @@ guide separately for instructions on how to do this. Should you install these d into non-standard locations you can direct portcullis to them by using the following options when running the configure script. - - ```--with-boost``` - for specifying a custom boost installation directory - - ```--with-zlib``` - for specifying a custom zlib installation directory + - ``--with-boost`` - for specifying a custom boost installation directory + - ``--with-zlib`` - for specifying a custom zlib installation directory -Note there is not option for specifying a custom pthreads or samtools location. -We assume pthreads is correctly installed and configured for your system already. In most cases -it will be. For samtools, we just require the executable to be on the path. +Note there is not option for specifying a custom *pthreads* or *samtools* location. +We assume *pthreads* is correctly installed and configured for your system already. In most cases +it will be. For *samtools*, we just require the executable to be on the path. -If the user has sphinx installed then documentation will also be built along with -the software. If sphinx is not detected then the documentation building stage is +If the user has *sphinx* installed then documentation will also be built along with +the software. If *sphinx* is not detected then the documentation building stage is skipped and documentation won't be available locally, although it can still be found at: https://portcullis.readthedocs.org/en/latest/ -Boost is statically linked and doesn't need to be available at runtime. zlib and pthreads are -dynamically linked so will need to be on your LD_LIBRARY_PATH, +Boost is statically linked and doesn't need to be available at runtime. *zlib* and *pthreads* are +dynamically linked so will need to be on your ``LD_LIBRARY_PATH``, or in one of the automatically searched lib directories in order for portcullis to dynamically link them at runtime. No other non-system libraries need linking at runtime. @@ -53,27 +53,27 @@ to dynamically link them at runtime. No other non-system libraries need linking Internal Dependencies --------------------- -Portcullis contains HTSlib and Ranger (a random forest implementation) in the source tree. The user does -not need to do anything special to handle htslib and ranger as these are automatically +Portcullis contains *HTSlib* and *Ranger* (a random forest implementation) in the source tree. The user does +not need to do anything special to handle *htslib* and *ranger* as these are automatically built and managed inside portcullis. Compilation and Installation ---------------------------- -First change into the portcullis root directory and run ```./configure```, providing -any options you feel are appropriate. By default the installation directory is "/usr/local", +First change into the portcullis root directory and run ``./configure``, providing +any options you feel are appropriate. By default the installation directory is ``/usr/local``, so the portcullis executable would be found at "/usr/local/bin" by default. If you want to change this use the ``--prefix`` option as previously described. For a full -list of configuration options type ```./configure --help```. +list of configuration options type ``./configure --help``. -Next compile the software. This can be done by typing ```make```. The compiles +Next compile the software. This can be done by typing ``make``. The compiles all internal dependencies and portcullis itself. To check the code compiled correct and is operating as expected you can optionally -type ```make check``` to runs some tests. This includes unit tests for HTSlib, +type ``make check`` to runs some tests. This includes unit tests for HTSlib, which are embedded in the portcullis source tree. To run only portcullis -unit tests go into the ``tests`` subdirectory and run ```make check``` there. +unit tests go into the ``tests`` subdirectory and run ``make check`` there. Finally to install the compiled code to the specified (or default) installation -directory type ```make install```. +directory type ``make install``. diff --git a/doc/source/quickstart.rst b/doc/source/quickstart.rst index 3467cfc1..2b67f383 100644 --- a/doc/source/quickstart.rst +++ b/doc/source/quickstart.rst @@ -3,7 +3,7 @@ Quickstart ========== -For the impatient, just use ```portcullis full -t ()+``` +For the impatient, just use ``portcullis full -t ()+`` to get up and running. This runs the following subtools in order: * Prepare diff --git a/doc/source/using.rst b/doc/source/using.rst index e622e603..9c18afda 100644 --- a/doc/source/using.rst +++ b/doc/source/using.rst @@ -4,9 +4,9 @@ Using Portcullis ================ Portcullis is a C++11 program containing a number of subtools which can be used in -isolation or as part of a pipeline. Typing ```portcullis --help``` will show a +isolation or as part of a pipeline. Typing ``portcullis --help`` will show a list of the available subtools. Each subtool has its own help system which you -can access by typing ```portcullis --help```. +can access by typing ``portcullis --help``. The list of subtools present in portcullis are listed below in order. A more detailed description of each subtool follows in the subsequent sections: @@ -151,8 +151,8 @@ for deriving a custom filter profile. The rules can be combined using logic operations (and / or / not, etc) and applied to the full set of input junctions. -Here's an example set of rules that must all be satisfied to pass this filter: -:: +Here's an example set of rules that must all be satisfied to pass this filter:: + { "parameters": { "M4-nb_rel_aln": {