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Improved README and documentation
Better checking of python dependencies
Enforcing static linking of kat_jellyfish and kat libraries to executable
Better checking of sequence files, now kat can detect fasta and fastq files for kmer counting, even without a known extension.
Generic installation description can be found in the INSTALL file. There are two ways to install KAT from source, either by cloning the git repository, or by downloading a distributable package, the later method is generally recommended as it reduces the number of installation steps and dependencies required to be on your system.
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Installing from distributable:
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- Confirm dependencies are installed and configured:
- Option 1 (preferred) python3, with matplotlib. We recommend installing anaconda3 as this has all the required packages preinstalled.
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- Option 2 gnuplot
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- Optional - Sphinx documentation V1.3+ (comes with anaconda3)
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- Download tarball from https://github.com/TGAC/KAT/releases
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There are two ways to install KAT from source, either by cloning the git repository, or by downloading a distributable package, the later method is generally recommended as it reduces the number of installation steps and dependencies required to be on your system.
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When installing from distributable first confirm dependencies are installed and configured:
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-**GCC** V4.8+
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-**make**
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-**libtool** V2.4.2+
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-**pthreads** (probably already installed)
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-**Boost** (*system*,*filesystem*,*program_options*,*chrono*,*timer*) V1.53+. KAT will statically link boost libraries when possible so please make sure you have boost static libraries built on your system.
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-**Sphinx-doc** V1.3+ (Optional: only required for building the documentation. Sphinx comes with anaconda3, however if not using anaconda3 then install according to the instructions on the sphinx website: [http://www.sphinx-doc.org/en/stable/instructions](http://www.sphinx-doc.org/en/stable/instructions)))
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In addition, KAT can only produce plots if one of the following plotting engines is installed:
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- Option 1 (preferred): **python3, with matplotlib**. We recommend installing anaconda3 as this has all the required packages pre-installed, otherwise we need a python3 installation with development libraries and the *scipy* and *numpy* packages installed.
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- Option 2: **gnuplot**. This will produce basic plots but will not be as rich and detailed as with python3.
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Then proceed with the following steps:
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- Download the latest tarball from here: [https://github.com/TGAC/KAT/releases](https://github.com/TGAC/KAT/releases). NOTE: Please make sure not to download the github source code zips. The KAT distributables have the following filename format ```kat-<version>.tar.gz```.
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- Decompress and untar: ```tar -xvf kat-<version>.tar.gz```
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- Change into directory: ```cd kat-x.x.x```
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- Generate makefiles and confirm dependencies: ```./configure```
@@ -47,22 +53,24 @@ Installing from distributable:
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- Install: ```sudo make install```
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Installing from cloned repository
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- 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.
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- "cd" into root directory of the installation
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Should you wish to install from a cloned git repository instead, do the following:
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- Ensure these tools are correctly installed and available on your system:
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- autoconf V2.53+
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- automake V1.11+
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- **autoconf** V2.53+
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- **automake** V1.11+
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- 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.
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- "cd" into root directory of the installation
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- Create configuration script by typing: ```./autogen.sh```.
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- Follow all steps described in "Installing from a distributable" (except for the download and decompress tarball steps).```
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- Follow all steps described in "Installing from a distributable" (except for the download and decompress tarball steps).
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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
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Type ```./configure --help``` for full details.
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KAT can also make plots. To enable plotting functionality we require either python3,
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As already mentioned KAT can also make plots but requires external software to be
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available to do this. To enable plotting functionality we require either python3,
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with numpy, scipy and matplotlib packages installed. The python installation
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must come with the python shared library, on debian systems you can install this
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with "sudo apt-get install python3-dev". If you don't already have python3 installed on your system
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produce nicer results.
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The type of plotting engine used will be determined when running the configure
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script, which will select the first engine detected in the following order: python, gnuplot, none.
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There is currently no way to select the plotting directory from a custom location,
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script, which will select the first engine detected in the following order: python,
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gnuplot, none. There is currently no way to select the plotting directory from a custom location,
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so the plotting system needs to be properly installed and configured on your
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system: i.e. python3 or gnuplot must be available on the PATH.
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@@ -106,10 +114,11 @@ GNU GPL V3. See COPYING file for more details.
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##Cite:
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The KAT paper is currently in submission. In the meantime, if you use our software
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and wish to cite us please use our bioRxiv preprint:
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If you use KAT in your work and wish to cite us please use the following citation:
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Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733
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Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, and Bernardo J. Clavijo.
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**KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies.**
AC_ARG_ENABLE([gnuplot], AS_HELP_STRING([--enable-gnuplot], [Enable gnuplot plotting even if python matplotlib is available]), enable_gnuplot="yes", enable_gnuplot="no")
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AM_PATH_PYTHON([], [], AC_MSG_ERROR([Python interpreter not found.]))
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#AM_PATH_PYTHON([], [], AC_MSG_ERROR([Python interpreter not found.]))
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AX_PYTHON_DEVEL([>= '3.1'])
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pybin=python${PYTHON_VERSION}
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pymod_good="no"
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if [[ -n "${PYTHON_VERSION}" ]]; then
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if [[ -z "${PYTHON_EXTRA_LIBS}" ]]; then
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pymod_good="no"
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AC_MSG_WARN([Python3 detected but Python3 development library was not found. If you wish to use python plotting please install python3 library. e.g. "sudo apt-get install python3-dev" on debian systems.])
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@@ -46,7 +46,7 @@ Citing
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The KAT paper is currently in submission. In the meantime, if you use our software
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and wish to cite us please use our bioRxiv preprint:
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Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733
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`Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733<http://biorxiv.org/content/early/2016/07/19/064733>`_
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======
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Should you discover any issues with spectre, or wish to request a new feature please raise a `ticket here <https://github.com/TGAC/KAT/issues>`_.
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