README

This is the source repository for the docker image
vimalkvn/qiime.

This image has QIIME 1.9.1 installed.

Notes:

• Based on Ubuntu 14.04.
• R (latest stable version for Ubuntu 14.04 from CRAN) and
  packages - ape, biom, optparse, RColorBrewer, randomForest, vegan, DESeq2
  and metagenomeSeq.
• Python 2 and QIIME python dependencies (numpy, matplotlib).
• All other dependencies installed using qiime-deploy.

Run this container

docker run --rm vimalkvn/qiime /bin/bash -c \
"source /opt/qiime_deps/activate.sh;print_qiime_config.py"

or use the included run-qiime wrapper script.

Todo

print_qiime_config.py -tf should pass with the exception of the test for finding
usearch. Possibly users can then save the usearch binary in the current
directory and it can be added to the PATH.