Modules
The BiomolecularStructures package provides several Bioinformatics-related modules:
- WebBLAST - A module to communicate with the NCBI/EBI BLAST servers.
- Kabsch - Superimposing protein structures
- PDB - Utility functions for parsing PDB files
- Plot - Rudimentary plotting of matrices of atomic coordinates
- Mafft - Julia API for multisequence alignment with MAFFT
- Modeller - Functions and scripts to use MODELLER with Julia
Documentation is available here: BiomolecularStructures
Binary Dependencies
The build script should take care of the BioPython dependency. Install MAFFT with sudo apt-get install mafft (or equivalent for other package managers) Modeller needs to be installed manually.
As the available MAFFT version may be different from the one we have tested with and we can't guarantee reproducibly working tests, the tests are disabled by default. You can reenable them by uncommenting the corresponding line in test/runtest.jl:
include(Pkg.dir("BiomolecularStructures", "test", "mafft.jl"))
Troubleshooting julia v0.5-dev
Package fails to build
ERROR: Build process failed.
INFO: Building HttpParser
ERROR: Build process failed.
Connecting to cache.julialang.org (cache.julialang.org)|52.91.20.35|:443... connected.
ERROR: no certificate subject alternative name matches
requested host name `cache.julialang.org'.
To connect to cache.julialang.org insecurely, use `--no-check-certificate'.
===============================[ ERROR: MbedTLS ]===============================
LoadError: failed process: Process(`wget -O /home/vagrant/.julia/v0.5/MbedTLS/deps/downloads/mbedtls-2.1.1-apache.tgz https://cache.julialang.org/https://tls.mbed.org/download/mbedtls-2.1.1-apache.tgz`, ProcessExited(5)) [5]
when building MbedTLS, download the file manually (change home directory) and then build the package:
wget --no-check-certificate -O /home/vagrant/.julia/v0.5/MbedTLS/deps/downloads/mbedtls-2.1.1-apache.tgz https://cache.julialang.org/https://tls.mbed.org/download/mbedtls-2.1.1-apache.tgz
Pkg.build("BiomolecularStructures")
Note: This a workaround, not a fix for MbedTLS
cmake command not found. installing cmake is required for building from source.
===============================[ ERROR: MbedTLS ]===============================
LoadError: failed process: Process(`./cmake_check.sh`, ProcessExited(1)) [1]
while loading /home/vagrant/.julia/v0.5/MbedTLS/deps/build.jl, in expression starting on line 69
================================================================================
Install cmake with sudo apt-get install cmake
Pkg.test("BiomolecularStructures") failing
ERROR: LoadError: LoadError: LoadError: LoadError: Failed to precompile PyPlot to /home/vagrant/.julia/lib/v0.5/PyPlot.ji
This seems to be an issue of how precompilation of dependencies is handled (see this issue: https://github.com/JuliaLang/julia/issues/14193) and does not happen reliably. Try running julia with --precompiled=yes or try precompiling the failing modules manually, e.g. Base.compilecache("Colors"), Base.compilecache("HttpCommon") and runPkg.test("BiomolecularStructures") again`
MAFFT test fails under Ubuntu 12.04 LTS
If mafft does not work (e.g. the mafft.jl test) and you get this output:
correctly installed?
mafft binaries have to be installed in $MAFFT_BINARIES
or the /build/buildd/mafft-6.850/debian/mafft/usr/lib/mafft/lib/mafft directory.
... you have a broken package. This is fixed in newer Ubuntu LTS releases.
Note about mafft tests
The mafft tests are disabled for v0.5 as i cannot get them to run reliably (tests fail or pass depending on unknown conditions).
Changelog
[0.2.3]
- fixes a bug in the Kabsch module (generated wrong RMSD values). See #19 for details.
[0.2.0]
- julia v0.5 compatibility - note: unstable, using the package with v0.5 may require manual fixes, see troubleshooting
[0.1.0]
- julia v0.4 compatibility
[0.0.1]
- initial release
A Bioinformatics WS 2014/15 course project by Simon Malischewski, Henning Schumann. Supervision by Prof. Dr. Daniel Hoffmann.
