Commit 318c3381 authored by Martin Frith's avatar Martin Frith
Browse files

Document ARM compilation (thanks: Alicia Clum)

parent 03dd5a89
......@@ -23,8 +23,9 @@ Usage
-----
Please see the cookbook_. **Warning:** this documentation may not
apply to older versions of LAST! You can see your version with
``lastal --version``.
apply to older versions of LAST! You can see your version with::
lastal --version
Install
-------
......@@ -38,8 +39,16 @@ into the downloaded directory and type::
This assumes you have a C++ compiler. On Linux, you might need to
install a package called "g++". On Mac, you might need to install
command-line developer tools. On Windows, you might need to install
Cygwin. (It's possible to specify a compiler like this:
``make CXX=MyOtherCompiler``.)
Cygwin. You might also need to install something like "zlib-devel".
For ARM CPUs, the default "make" seems to work in some cases but not
others (sigh). This seems to be good for ARM::
make CXXFLAGS="-mcpu=native -O3 -pthread"
It's possible to specify a compiler like this: ``make CXX=MyOtherCompiler``.
If you re-run ``make`` in different ways, it may be good to do ``make clean``
first, to remove any previously-made files.
The programs are in the ``bin`` directory. For convenient usage, set
up your computer to find them automatically. Some possible ways:
......
......@@ -159,10 +159,10 @@ Options ``-a`` and ``-b`` can read annotations in these formats:
* AGP_, gap.txt: Unsequenced gaps are shown, but only if the gap
covers at least one whole pixel.
You can use these options multiple times, e.g. ``-a stuff.bed -a
more.bed -a rmsk.txt``. Annotations look good only if reasonably
sparse, e.g. you can't sensibly view 20000 gene annotations in one
small dotplot.
You can use these options multiple times, e.g.
``-a stuff.bed -a more.bed -a rmsk.txt``. Annotations look good only
if reasonably sparse, e.g. you can't sensibly view 20000 gene
annotations in one small dotplot.
Choosing sequences
------------------
......
CXXFLAGS = -msse4 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS
CXXFLAGS = -msse4 -O3 -std=c++11 -pthread
all:
@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
......
CXXFLAGS = -msse4 -O3 -Wall -g -std=c++11 -pthread -DHAS_CXX_THREADS
CXXFLAGS = -msse4 -O3 -Wall -g -std=c++11 -pthread
# -fomit-frame-pointer ?
# The number of symbol types that we can keep in sequences (e.g. 20
# amino acids, plus ambiguous ones, in upper & lower case, plus one
# delimiter):
ALPHABET_CAPACITY = 66
CPPF = -DALPHABET_CAPACITY=$(ALPHABET_CAPACITY) $(CPPFLAGS)
CPPF = -DALPHABET_CAPACITY=$(ALPHABET_CAPACITY) -DHAS_CXX_THREADS $(CPPFLAGS)
CFLAGS = -Wall -O2
......
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