================= Quickstart Guide ================= Installation and configuration ============================== With Bioconda ------------- conda install segway Generic installation ---------------- 1. To install Segway first install `GMTK `_, and install `HDF5 `_,. Then run this command from :program:`bash`:: pip install segway 2. If you are using SGE, your system administrator must set up a ``mem_requested`` resource for Segway to work. This can be done by installing Segway and then running ``python -m segway.cluster.sge_setup``. Acquiring data ============== 3. Observation data is stored with the genomedata system. . There is a small Genomedata archive for testing that comes with Segway, that is used in the below steps. You can get it using:: wget http://pmgenomics.ca/hoffmanlab/proj/segway/2011/test.genomedata Running Segway ============== 4. Use the ``segway train`` command to discover patterns in the test data. Here, we specify that we want Segway to discover four unique patterns:: segway --num-labels=4 train test.genomedata traindir 5. Use the ``segway identify`` command to create the segmentation, which partitions the genome into regions labeled with one of the four discovered patterns:: segway identify test.genomedata traindir identifydir .. note:: This example spawns jobs that will run sequentially due to small segment size. See the :option:`--split-sequences` option for dividing segments into smaller pieces. Results ======= 6. The ``identifydir/segway.bed.gz`` file has each segment as a separate line in the BED file, and can be used for further processing. 7. The ``identifydir/segway.layered.bed.gz`` file is designed for easier visualization on a genome browser. It has thick lines where a segment is present and thin lines where it is not. This is not as easy for a computer to parse, but it is more useful visually. 8. You can also perform further analysis of the segmentation and trained parameters using Segtools .