Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 23:545f23776953 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
| author | pjbriggs |
|---|---|
| date | Wed, 29 Aug 2018 10:57:51 -0400 |
| parents | eb7d118dd322 |
| children | fe354f5dd0ee |
| files | amplicon_analysis_pipeline.xml tool_dependencies.xml |
| diffstat | 2 files changed, 23 insertions(+), 7 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.xml Wed Jul 04 06:56:48 2018 -0400 +++ b/amplicon_analysis_pipeline.xml Wed Aug 29 10:57:51 2018 -0400 @@ -1,8 +1,12 @@ <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1"> <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> <requirements> - <!-- amplicon_analysis_pipeline not available in bioconda --> + <!-- non-bioconda dependencies --> <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement> + <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement> + <requirement type="package" version="1.2.22">uclust-qiime</requirement> + <requirement type="package">fasta_number</requirement> + <!-- bioconda dependencies --> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.11">cutadapt</requirement> <requirement type="package" version="1.33">sickle-trim</requirement> @@ -14,13 +18,8 @@ <requirement type="package" version="2.2.26">blast-legacy</requirement> <requirement type="package" version="0.2.4">fasta-splitter</requirement> <requirement type="package" version="2.2">rdp_classifier</requirement> + <requirement type="package" version="1.1.3">vsearch</requirement> <requirement type="package" version="3.2.1">R</requirement> - <requirement type="package" version="1.1.3">vsearch</requirement> - <requirement type="package" version="1.2.22">uclust-qiime</requirement> - <!-- microbiomeutil not available in bioconda --> - <requirement type="package" version="2010-04-29">microbiomeutil</requirement> - <!-- fastq_number not available in bioconda --> - <requirement type="package">fasta_number</requirement> </requirements> <stdio> <exit_code range="1:" />
--- a/tool_dependencies.xml Wed Jul 04 06:56:48 2018 -0400 +++ b/tool_dependencies.xml Wed Aug 29 10:57:51 2018 -0400 @@ -35,6 +35,23 @@ </install> </package> <!-- + microbiomeutil provides ChimeraSlayer + --> + <package name="microbiomeutil-chimeraslayer" version="2010-04-29"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action> + <action type="move_directory_files"> + <source_directory>ChimeraSlayer</source_directory> + <destination_directory>$INSTALL_DIR/ChimeraSlayer</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/ChimeraSlayer</environment_variable> + </action> + </actions> + </install> + </package> + <!-- uclust required for QIIME/pyNAST License only allows this version to be used with those two packages See: