Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison README.rst @ 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 b5e43dfe07ac
comparison
equal deleted inserted replaced
4:013bf1e2cc8f 5:bbfc9638ba84
192 - cutadapt 1.8.1 192 - cutadapt 1.8.1
193 - sickle-trim 1.33 193 - sickle-trim 1.33
194 - bioawk 1.0 194 - bioawk 1.0
195 - fastqc 0.11.3 195 - fastqc 0.11.3
196 - R 3.2.0 196 - R 3.2.0
197 197 - spades 3.5.0
198 Some dependencies are available but with the "wrong" versions: 198 - qiime 1.8.0
199 199 - blast-legacy 2.2.26
200 - spades (need 3.5.0) 200 - vsearch 1.1.3
201 - qiime (need 1.8.0) 201 - fasta-splitter 0.2.4
202 - blast (need 2.2.26) 202 - rdp_classifier 2.2
203 - vsearch (need 1.1.3)
204 203
205 The following dependencies are currently unavailable: 204 The following dependencies are currently unavailable:
206 205
207 - fasta_number (need 02jun2015) 206 - fasta_number (need 02jun2015)
208 - fasta-splitter (need 0.2.4)
209 - rdp_classifier (need 2.2)
210 - microbiomeutil (need r20110519) 207 - microbiomeutil (need r20110519)
211 208
212 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be 209 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
213 handled outside of Galaxy's dependency management systems.) 210 handled outside of Galaxy's dependency management systems.)
214 211
216 ======= 213 =======
217 214
218 ========== ====================================================================== 215 ========== ======================================================================
219 Version Changes 216 Version Changes
220 ---------- ---------------------------------------------------------------------- 217 ---------- ----------------------------------------------------------------------
218 1.2.2.1 Update to get dependencies from bioconda
221 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes 219 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
222 jackknifed analysis which is not captured by Galaxy tool) 220 jackknifed analysis which is not captured by Galaxy tool)
223 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds 221 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
224 option to use the Human Oral Microbiome Database v15.1, and 222 option to use the Human Oral Microbiome Database v15.1, and
225 updates SILVA database to v123) 223 updates SILVA database to v123)