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Glimmer3 has been installed manually in the BioITeam bin $BI/bin since it is not offered as a module on TACC.
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{hidden-data} Remember from day 2 that there are three general steps for installing a linux tool.
1. Download and uncompress the Glimmer3 source code
{code}
login1$ cdh
login1$ wget http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz
login1$ tar xzf glimmer302.tar.gz
{code}
2. Compile the Glimmer3 programs and copy them to {{\~/local/bin/}}
{code}
login1$ cd glimmer3.02/src/
login1$ make
login1$ cd ..
login1$ cp bin/* ~/local/bin/
{code}
3. Your $PATH variable should have been set up on day 2 to look in {{\~/local/bin/}} for executables. If not, update your {{$HOME/.profile_user}} file with the following line.
{code}
export PATH="$HOME/local/bin:$PATH"
{code}
{hidden-data} |
Running Glimmer3
Running Glimmer3 is a two-step process. First, a probability model of coding sequences, called an interpolated context model or ICM, must be built. Once that has been built, the glimmer3 program itself is run to analyze the assembled genome and make gene predictions.
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We'll run Glimmer on a de novo assembly of the bacterium Acinetobacter baumannii. First copy the contigs.fa file that velvet produced, and then execute the run_glimmer.sh script. This script preprocesses the contigs.fa file and calls the g3-from-scratch.csh script that was prepackaged with glimmer3. Several files will be created, but the one containing the predicted genes is called contigs.fa.glimmer.predict.genes.
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fa
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glimmer
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predict.genes.
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cdw mkdir glimmer_example cd glimmer_example cp $BI/ngs_course/velvet/real_set/contigs.fa . run_glimmer.sh contigs.fa |
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