Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 45:4bfa62618f7c draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 3dcfecb6c83d655529be44366d9e55913df9dffd
| author | pjbriggs |
|---|---|
| date | Wed, 11 Dec 2019 13:45:05 +0000 |
| parents | 213b5cdecb70 |
| children | 8d5fe964f61f |
| files | amplicon_analysis_pipeline.xml install_amplicon_analysis-1.3.5.sh |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.xml Mon Dec 09 13:00:31 2019 +0000 +++ b/amplicon_analysis_pipeline.xml Wed Dec 11 13:45:05 2019 +0000 @@ -85,7 +85,7 @@ cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" && ## OTU table heatmap - cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}"" && + cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}" && ## HTML outputs
--- a/install_amplicon_analysis-1.3.5.sh Mon Dec 09 13:00:31 2019 +0000 +++ b/install_amplicon_analysis-1.3.5.sh Wed Dec 11 13:45:05 2019 +0000 @@ -88,6 +88,9 @@ wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR} echo Installed conda in ${CONDA_DIR} + echo -n "Adding conda bin to PATH..." + export PATH=${CONDA_BIN}:$PATH + echo "ok" # Reset the conda version to a known working version # (to avoid problems observed with e.g. conda 4.7.10) echo "" @@ -100,9 +103,6 @@ echo -n "Rewriting conda shebangs..." rewrite_conda_shebangs echo "ok" - echo -n "Adding conda bin to PATH..." - export PATH=${CONDA_BIN}:$PATH - echo "ok" cd $cwd rm -rf $wd/* rmdir $wd