Friday, July 19, 2013

summarize_taxa_through_plots give json error

When running Qiime's summarize_taxa_through_plots.py, I get an error No JSON object could be decoded. I fixed this by making sure that the input OTU table was in biom format and had "taxonomy" in place of the "consensus lineage" header output by make_otu_table.

running summarize_taxa_through_plots on cluster

I git-cloned Qiime into ~/src. I installed with --prefix=/home/username/local and then had to change the line in ~/.qiime_config to qiime_scripts_dir <tab> /home/username/local/bin.

In my ~/src I git-cloned qcli and installed it with --prefix=/home/username/local. I had to add /home/username/local/lib/python2.7/site-packages, /home/username/local/bin, and /home/username/local/lib to my $PYTHONPATH.

I also had to load the module matplotlib.

Thursday, July 18, 2013

changing default shell

To change from tcsh to bash:

chsh -p /bin/bash my_username

Maybe you need usermod rather than chsh. This modifies /etc/passwd.