Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 21:092e39db5f59 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit bae32168fbfd40305a4768b889a8e7689e5987e3-dirty
| author | pjbriggs |
|---|---|
| date | Wed, 04 Jul 2018 05:57:44 -0400 |
| parents | 8d8aad8752f9 |
| children | eb7d118dd322 |
| files | amplicon_analysis_pipeline.py tool_dependencies.xml |
| diffstat | 2 files changed, 15 insertions(+), 0 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.py Tue Jul 03 09:33:34 2018 -0400 +++ b/amplicon_analysis_pipeline.py Wed Jul 04 05:57:44 2018 -0400 @@ -225,6 +225,15 @@ print "-- set RDP_JAR_PATH: %s" % os.environ["RDP_JAR_PATH"] else: sys.stderr.write("Missing 'rdp_classifier.jar'\n") + # Set up qiime_config file + qiime_config_file = os.path.abspath("qiime_config") + with open(qiime_config_file,'w') as qiime_config: + # Set qiime_scripts_dir + qiime_config.write("qiime_scripts_dir: %s" % + os.path.dirname( + find_executable("single_rarefaction.py"))) + os.environ["QIIME_CONFIG_FP"] = qiime_config_file + print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"] # Construct the pipeline command print "Amplicon analysis: constructing pipeline command"
--- a/tool_dependencies.xml Tue Jul 03 09:33:34 2018 -0400 +++ b/tool_dependencies.xml Wed Jul 04 05:57:44 2018 -0400 @@ -34,6 +34,12 @@ </actions> </install> </package> + <!-- + uclust required for QIIME/pyNAST + License only allows this version to be used with those two packages + See: + http://drive5.com/uclust/downloads1_2_22q.html + --> <package name="uclust-qiime" version="1.2.22"> <install version="1.0"> <actions>