Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 34:3512b135ecb0 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty
| author | pjbriggs |
|---|---|
| date | Mon, 15 Oct 2018 10:40:41 -0400 |
| parents | c4cde1f435f4 |
| children | 44f5057fc878 |
| files | amplicon_analysis_pipeline.xml tool_dependencies.xml |
| diffstat | 2 files changed, 9 insertions(+), 88 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.xml Wed Oct 10 10:57:42 2018 -0400 +++ b/amplicon_analysis_pipeline.xml Mon Oct 15 10:40:41 2018 -0400 @@ -2,25 +2,7 @@ <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> <requirements> <!-- non-bioconda dependencies --> - <requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement> - <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement> - <requirement type="package" version="1.2.22">uclust-qiime</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> - <requirement type="package" version="1.0">bioawk</requirement> - <requirement type="package" version="2.8.1">pandaseq</requirement> - <requirement type="package" version="3.5.0">spades</requirement> - <requirement type="package" version="0.11.3">fastqc</requirement> - <requirement type="package" version="1.8.0">qiime</requirement> - <requirement type="package" version="1.0">libgfortran</requirement> - <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> - <!-- toolshed dependencies --> - <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.2.3">amplicon_analysis_pipeline-all</requirement> </requirements> <stdio> <exit_code range="1:" />
--- a/tool_dependencies.xml Wed Oct 10 10:57:42 2018 -0400 +++ b/tool_dependencies.xml Mon Oct 15 10:40:41 2018 -0400 @@ -1,80 +1,19 @@ <?xml version="1.0"?> <tool_dependency> - <package name="amplicon_analysis_pipeline" version="1.2.3"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/MTutino/Amplicon_analysis/archive/v1.2.3.tar.gz</action> - <action type="move_file"> - <source>Amplicon_analysis_pipeline.sh</source> - <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> - </action> - <action type="move_file"> - <source>FIRST_STEP.sh</source> - <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> - </action> - <action type="move_file"> - <source>VSEARCH.sh</source> - <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> - </action> - <action type="move_file"> - <source>STAT_ANALYSIS.sh</source> - <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> - </action> - <action type="move_file"> - <source>THIRD_STEP.sh</source> - <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> - </action> - <action type="move_directory_files"> - <source_directory>uc2otutab</source_directory> - <destination_directory>$INSTALL_DIR/Amplicon_analysis_pipeline/uc2otutab</destination_directory> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable> - </action> - </actions> - </install> - </package> - <!-- - microbiomeutil provides ChimeraSlayer - --> - <package name="microbiomeutil-chimeraslayer" version="2010-04-29"> + <package name="amplicon_analysis_pipeline-all" version="1.2.3"> <install version="1.0"> <actions> - <action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action> - <action type="move_directory_files"> - <source_directory>ChimeraSlayer</source_directory> - <destination_directory>$INSTALL_DIR/ChimeraSlayer</destination_directory> + <action type="download_file">https://raw.githubusercontent.com/pjbriggs/Amplicon_analysis-galaxy/88289d6e8376bc94eb1a86391c3de9a81b1aa8a0/install_amplicon_analysis.sh</action> + <action type="chmod"> + <file mode="755">./install_amplicon_analysis.sh</file> + </action> + <action type="shell_command"> + ./install_amplicon_analysis.sh $INSTALL_DIR </action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/ChimeraSlayer</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Amplicon_analysis-1.2.3/bin</environment_variable> </action> </actions> </install> </package> - <!-- - uclust required for QIIME/pyNAST - License only allows this version to be used with those two packages - See: - http://drive5.com/uclust/downloads1_2_22q.html - --> - <package name="uclust-qiime" version="1.2.22"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://drive5.com/uclust/uclustq1.2.22_i86linux64</action> - <action rename_to="uclust" type="move_file"> - <source>uclustq1.2.22_i86linux64</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/bin/uclust</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - </package> - <package name="R" version="3.2.1"> - <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> </tool_dependency>