A flexible framework for rapid genome analysis and interpretation.
See versions of speedseq which are available:
$ module avail speedseq
Load and run speedseq:
$ module load speedseq/0.1.2 $ speedseq
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/speedseq/0.1.2 $ sudo chown aorth /export/apps/speedseq/0.1.2 $ git clone -b v0.1.2 --recursive https://github.com/hall-lab/speedseq.git /export/apps/speedseq/0.1.2 $ cd /tmp $ wget https://www.python.org/ftp/python/2.7.13/Python-2.7.13.tar.xz $ tar xf Python-2.7.13.tar.xz $ cd Python-2.7.13 $ ./configure --prefix=/export/apps/speedseq/0.1.2 --enable-shared --with-threads --with-computed-gotos --enable-optimizations --with-lto --enable-ipv6 $ make -j4 $ make install $ make maninstall $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/speedseq/0.1.2/lib $ export PATH=/export/apps/speedseq/0.1.2/bin:$PATH $ export PYTHONHOME=/export/apps/speedseq/0.1.2 $ curl https://bootstrap.pypa.io/get-pip.py | python $ pip install numpy $ pip install pysam $ pip install scipy $ cd /export/apps/speedseq/0.1.2 # Remove -lCint from ROOTLIBS in src/cnvnator/Makefile # Add -std=c++11 to CXX in src/cnvnator/Makefile # See: https://github.com/abyzovlab/CNVnator/issues/9 # See: https://github.com/hall-lab/speedseq/issues/77 $ module load root/6.08.06 $ make $ sudo chown -R root:root /export/apps/speedseq
Note: compiled on CentOS 7 because it needs quite a bit of modern dependencies, so make sure to run it from a compute node that is running CentOS 7!
Also, because speedseq requires a Python with several modules installed, I decided to install Python into the speedseq root so that speedseq could have a dedicated Python. This is the reason the install above is slightly out of order (cloning the speedseq dir first, then installing the Python requirement into it).