Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 30:18e6427c5e4a draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa
| author | pjbriggs |
|---|---|
| date | Tue, 02 Oct 2018 08:58:13 -0400 |
| parents | 31b7950136ed |
| children | b195d76c70e1 |
| files | README.rst amplicon_analysis_pipeline.py |
| diffstat | 2 files changed, 1 insertions(+), 42 deletions(-) [+] |
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--- a/README.rst Mon Oct 01 07:31:44 2018 -0400 +++ b/README.rst Tue Oct 02 08:58:13 2018 -0400 @@ -177,46 +177,6 @@ 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 ======= @@ -224,7 +184,7 @@ Version Changes ---------- ---------------------------------------------------------------------- 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install - dependencies from bioconda and via tool_dependencies.xml + 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
--- a/amplicon_analysis_pipeline.py Mon Oct 01 07:31:44 2018 -0400 +++ b/amplicon_analysis_pipeline.py Tue Oct 02 08:58:13 2018 -0400 @@ -101,7 +101,6 @@ for p in os.environ['PATH'].split(os.pathsep): exe = os.path.normpath( os.path.abspath(os.path.join(p,name))) - print "Checking %s" % exe if os.path.isfile(exe) and os.access(exe,os.X_OK): return exe return None