Blasr Installation Qs & As

Armin Töpfer edited this page Jun 11, 2018 · 25 revisions

How to build the latest blasr

Answer 1

Do you really need to build on your own? In general, we recommend you use the releases from Bioconda, as all libraries and runtime dependencies are taken care for you there, without requiring any compilation.

conda install -c bioconda blasr
Answer 2

BLASR can only be built using Meson, which uses Ninja as command invoking tool.

git clone git://github.com/PacificBiosciences/blasr.git
LDFLAGS="-L${PATH_TO_HDF5_ROOT}/lib -lhdf5_cpp -lhdf5" \
CPPFLAGS="-isystem ${PATH_TO_HDF5_ROOT}/include" \
meson -Dtests=false build .
ninja -C build
ninja -C build install

What is the minimum compiler version?

Answer

gcc-4.8.1, though several clang versions should work too.


What is the minimum HDF version?

Answer

hdf-1.8.18 or hdf-1.10, but newer is better.


Can I use an old compiler/environment?

Answer

Because we use C++11 features, you must upgrade your compiler. One way is to install installing devtoolset-3-toolchain, as in issue #91.


Why can't I pull from GitHub?

$ git clone git://github.com/PacificBiosciences/blasr_libcpp.git
Cloning into 'blasr_libcpp'...
fatal: unable to connect to github.com:
github.com[0: 192.30.252.130]: errno=Connection refused
Answer

You are probably behind a firewall. Try the slower https: URL:

$ git clone https://github.com/PacificBiosciences/blasr_libcpp.git

You do not necessarily need to modify blasr/.gitmodules. Instead, you can modify blasr/.git/config after running git submodule init.


Why do I have link errors involving ``?

Answer

This comes up a lot, since the g++ ABI changed with 5.0.

One of the solutions mentioned in those links should work for you. (See issue#125.)


How do I get past errors like "AttributeError: 'module' object has no attribute 'Distutils'" (Cython.Distutils)?

Answer

You could try pip install --upgrade setuptools_cython.

Better: We, along with some users, have had luck with Ananconda.

bash Anaconda2-2.4.1-Linux-x86_64.sh
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.