/galaxy/old/QIIMEPlots/createPlots.sh

https://gitlab.com/wurssb/NG-Tax · Shell · 25 lines · 7 code · 7 blank · 11 comment · 1 complexity · 171fef8c144ff92d80cb3500b55523ef MD5 · raw file 

    

  1. #!/bin/bash
    2. 

  2. 

  3. #As galaxy runs in a virtual env the user python path is reset... therefor I (jasper) used this uqly hacky solution... (for now...)
    4. 

  4. PYTHONPATH=/home/QIIME_deploy/qiime_180/qiime-galaxy-0.0.1-repository-c2814c3c/lib/:/home/QIIME_deploy/qiime_180/qiime-1.8.0-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/tax2tree-1.0-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/biom-format-1.3.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pynast-1.2.2-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pprospector-1.0.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/qiime-1.8.0-release/lib/:/home/QIIME_deploy/qiime_180/emperor-0.9.3-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/matplotlib-1.3.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/sphinx-1.0.4-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pyqi-0.3.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pycogent-1.5.3-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/MySQL-python-1.2.3-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/mpi4py-1.2.2-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/setuptools-0.6c11-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/gdata-2.0.17-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pysqlite-2.6.3-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/tornado-3.1.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/qcli-0.1.0-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/ipython-latest-repository-126bd580/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pyzmq-2.1.11-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/SQLAlchemy-0.7.1-release/lib/python2.7/site-packages:/home/QIIME_deploy/qiime_180/pysqlite-2.6.3-release/lib/:/home/QIIME_deploy/qiime_180/numpy-1.7.1-release/lib/python2.7/site-packages:
    5. 

  5. 

  6. #Get path of script
    7. 

  7. DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
    8. 

  8. 

  9. echo 'Summarize_taxa_though_plots'
    10. 

  10. summarize_taxa_through_plots.py -f -i $1 -o taxa_summary_test 2>&1
    11. 

  11. #/usr/bin/Rscript --vanilla $DIR/R/fastaFilesFromJson.R $1
    12. 

  12. 

  13. #echo 'clustalo'
    14. 

  14. #clustalo -i ./fasta_files/all_otus.fa --guidetree-out=./taxa_summary_test/all_otus_omega.tree --outfmt=clu --force
    15. 

  15. #sed -i s/";"/"|"/g ./taxa_summary_test/all_otus_omega.tree
    16. 

  16. #mkdir ./taxa_summary_test/treeFiles/
    17. 

  17. #for f in ./fasta_files/*; do name=$(basename $f); clustalo -i $f --guidetree-out=./taxa_summary_test/treeFiles/$name.tree --outfmt=clu --force; sed -i s/";"/"|"/g ./taxa_summary_test/treeFiles/$name.tree; done
    18. 

    19. 

  19. echo 'removing fasta_files'
    20. 

  20. #rm -R ./fasta_files
    21. 

    22. 

  22. #echo 'zipping'
    23. 

  23. zip -r taxa_summary_test.zip taxa_summary_test
    24. 

    25. 

  25. mv taxa_summary_test.zip $2
    26.