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khmer-protocols/mrnaseq/3-big-assembly.txt trinity installation #163
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Can you post the error that was printed to the terminal when read counting failed? |
Then ran Using gnu compiler for Inchworm and Chrysalis |
at
khmer-protocols/mrnaseq/3-big-assembly.txt
mkdir -p ${HOME}/src cd ${HOME}/src
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.4.tar.gz \ -O trinity.tar.gz tar xzf trinity.tar.gz cd trinityrnaseq*/ make |& tee trinity-build.log
Trinity subsequently fails. There seems to be a problem with Chrysalis installation. Trinity will start, and fail during read counting.
I used:
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz tar xzf Trinity-v2.4.0.tar.gz cd trinityrnaseq*/ make make plugins
Install java 1.8
sudo add-apt-repository ppa:webupd8team/java sudo apt-get update sudo apt-get install oracle-java8-installer
Install bowtie2
sudo apt-get install bowtie2
Test trinity
cd sample_data/test_Trinity_Assembly/ ./runMe.sh
and was successful.
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