comparison README.rst @ 30:18e6427c5e4a draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa

29:31b7950136ed

   These are both problems with Galaxy and not the tool, see
   https://github.com/galaxyproject/galaxy/issues/4490 and
   https://github.com/galaxyproject/galaxy/issues/1676

Appendix: availability of tool dependencies
===========================================

The tool takes its dependencies from the underlying pipeline script (see
https://github.com/MTutino/Amplicon_analysis/blob/master/README.md
for details).

As noted above, currently the ``install_tool_deps.sh`` script can be
used to manually install the dependencies for a local tool install.

In principle these should also be available if the tool were installed
from a toolshed. However it would be preferrable in this case to get as
many of the dependencies as possible via the ``conda`` dependency
resolver.

The following are known to be available via conda, with the required
version:

 - cutadapt 1.8.1
 - sickle-trim 1.33
 - bioawk 1.0
 - fastqc 0.11.3
 - R 3.2.0
 - spades 3.5.0
 - qiime 1.8.0
 - blast-legacy 2.2.26
 - vsearch 1.1.3
 - fasta-splitter 0.2.4
 - rdp_classifier 2.2

The following dependencies are currently unavailable:

 - R 3.2.1 (installed from the toolshed as the bioconda version
   has conflicts )
 - microbiomeutil (need r20110519)


(NB usearch 6.1.544 and 8.0.1623 are special cases which must be
handled outside of Galaxy's dependency management systems.)

History
=======

========== ======================================================================
Version    Changes
---------- ----------------------------------------------------------------------
1.2.3.0    Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
           dependencies from bioconda and via tool_dependencies.xml
1.2.2.0    Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
           jackknifed analysis which is not captured by Galaxy tool)
1.2.1.0    Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
           option to use the Human Oral Microbiome Database v15.1, and
           updates SILVA database to v123)

30:18e6427c5e4a

   These are both problems with Galaxy and not the tool, see
   https://github.com/galaxyproject/galaxy/issues/4490 and
   https://github.com/galaxyproject/galaxy/issues/1676

History
=======

========== ======================================================================
Version    Changes
---------- ----------------------------------------------------------------------
1.2.3.0    Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
           dependencies from bioconda and via tool_dependencies.xml.
1.2.2.0    Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
           jackknifed analysis which is not captured by Galaxy tool)
1.2.1.0    Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
           option to use the Human Oral Microbiome Database v15.1, and
           updates SILVA database to v123)