Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 2:43d6f81bc667 draft
Updated to Amplicon_Analysis_pipeline v1.2.2.
| author | pjbriggs |
|---|---|
| date | Wed, 13 Jun 2018 07:45:06 -0400 |
| parents | 1c1902e12caf |
| children | 3ab198df8f3f |
| files | README.rst amplicon_analysis_pipeline.xml install_tool_deps.sh |
| diffstat | 3 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/README.rst Wed Apr 25 03:54:00 2018 -0400 +++ b/README.rst Wed Jun 13 07:45:06 2018 -0400 @@ -218,6 +218,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +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 option to use the Human Oral Microbiome Database v15.1, and updates SILVA database to v123)
--- a/amplicon_analysis_pipeline.xml Wed Apr 25 03:54:00 2018 -0400 +++ b/amplicon_analysis_pipeline.xml Wed Jun 13 07:45:06 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.1.0"> +<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.0"> <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> <requirements> - <requirement type="package" version="1.2.1">amplicon_analysis_pipeline</requirement> + <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement> <requirement type="package" version="1.11">cutadapt</requirement> <requirement type="package" version="1.33">sickle</requirement> <requirement type="package" version="27-08-2013">bioawk</requirement>
--- a/install_tool_deps.sh Wed Apr 25 03:54:00 2018 -0400 +++ b/install_tool_deps.sh Wed Jun 13 07:45:06 2018 -0400 @@ -35,6 +35,9 @@ rm -rf $wd/* rmdir $wd } +function install_amplicon_analysis_pipeline_1_2_2() { + install_amplicon_analysis_pipeline $1 1.2.2 +} function install_amplicon_analysis_pipeline_1_2_1() { install_amplicon_analysis_pipeline $1 1.2.1 } @@ -689,7 +692,7 @@ mkdir -p $TOP_DIR fi # Install dependencies -install_amplicon_analysis_pipeline_1_2_1 $TOP_DIR +install_amplicon_analysis_pipeline_1_2_2 $TOP_DIR install_cutadapt_1_11 $TOP_DIR install_sickle_1_33 $TOP_DIR install_bioawk_27_08_2013 $TOP_DIR