Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

diff amplicon_analysis_pipeline.xml @ 5:bbfc9638ba84 draft

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First version with (partial) bioconda deps.
author pjbriggs
date Wed, 13 Jun 2018 08:39:26 -0400
parents 013bf1e2cc8f
children 45db1f97795c
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--- a/amplicon_analysis_pipeline.xml	Wed Jun 13 07:43:57 2018 -0400
+++ b/amplicon_analysis_pipeline.xml	Wed Jun 13 08:39:26 2018 -0400
@@ -1,20 +1,24 @@
-<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.0">
+<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 -->
     <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
+    <requirement type="package" version="2.7">python</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>
+    <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="2.2.26">blast</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="2.2">rdp_classifier</requirement>
     <requirement type="package" version="3.2.0">R</requirement>
     <requirement type="package" version="1.1.3">vsearch</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>