Frogs3.0.0

recipes/frogs/build.sh

@@ -11,7 +11,6 @@ mkdir -p $BINARY_HOME
 mkdir -p $LIB_HOME
 mkdir -p $LIBEXEC_HOME
 
-
 mv $SRC_DIR/* $FROGS_HOME
 
 #Make sure all css and js requests are https so reports work on https servers
@@ -22,4 +21,4 @@ ln -s $FROGS_HOME/app/*.html $BINARY_HOME
 ln -s $FROGS_HOME/app/*.Rmd $BINARY_HOME
 ln -s $FROGS_HOME/lib/* $LIB_HOME
 ln -s $FROGS_HOME/libexec/* $LIBEXEC_HOME
-ln -s $PREFIX/share/rdptools-2.0.2-0/classifier.jar $BINARY_HOME
+ln -s $PREFIX/share/rdptools-*/classifier.jar $BINARY_HOME

recipes/frogs/meta.yaml

@@ -1,53 +1,62 @@
 {% set name = "frogs" %}
-{% set version = "2.0.1" %}
+{% set version = "3.1.0" %}
+{% set phyloseq_extended_version = "0.99" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 3
+  number: 0
   skip: true  # [py3k]
 
+# 1) Uplaod FROGS source code
+# 2) Add phyloseq-extented lib from Mahendra Mariadassou to FROGS (lib/external-lib) :
 source:
-  url: https://github.com/oinizan/FROGS/archive/v{{ version }}.tar.gz
-  md5: da41b0950a750be2038cefa717edf9df
+  - url: https://github.com/geraldinepascal/FROGS/archive/v{{ version }}.tar.gz 
+    md5: 1a72f44e82517b6839a82cd677b98858 
+  - url: https://github.com/mahendra-mariadassou/phyloseq-extended/archive/v{{ phyloseq_extended_version }}.tar.gz
+    md5: 1ec072751503eebb791e876a60433120
+    folder: lib/external-lib
 
 requirements:
   host:
     - python
-    - rdptools >=2.0.2
+
   run:
+    - emboss 6.6.0
     - python
-    - scipy >=0.17.1
+    - scipy 1.1.0
     - perl
-    - perl-io-gzip >=0.20
-    - flash >=1.2.11
-    - cutadapt >=1.8.3
-    - swarm >=2.1.13
-    - vsearch >=2.4.3
-    - blast >=2.2.31
-    - rdptools >=2.0.2
+    - perl-io-gzip 0.20
+    - flash 1.2.11
+    - cutadapt 1.18
+    - swarm 2.2.2
+    - vsearch 2.9.1
+    - blast 2.7.1
+    - rdptools 2.0.2
     - util-linux # [linux]
-    - pynast >=1.2.2
-    - mafft >=7.310
-    - fasttree >=2.1.9
-    - r-base >=3.4.1
-    - r-phangorn >=2.2.0
-    - pandoc <2.0
-    - r-rmarkdown >=1.5
-    - bioconductor-phyloseq >=1.22.0
-    - r-plotly >=4.7.1
-    - r-gridextra >=2.2.1
-    - r-vegan <2.5
+    - mafft 7.407
+    - fasttree 2.1.10
+    - r-base 3.5.1
+    - r-phangorn 2.4.0
+    - pandoc 1.19.2.1
+    - r-rmarkdown 1.10
+    - bioconductor-phyloseq 1.24.2
+    - r-plotly 4.8.0
+    - r-gridextra 2.3
+    - itsx 1.1b
+    - pynast 1.2.2
 
 test:
   commands:
     - preprocess.py -h
     - clustering.py -h
     - remove_chimera.py -h
     - filters.py -h
+    - itsx.py -h
     - affiliation_OTU.py -h
+    - affiliation_postprocess.py -h
     - clusters_stat.py -h
     - affiliations_stat.py -h
     - biom_to_tsv.py -h
@@ -63,4 +72,4 @@ test:
 about:
   home: https://github.com/geraldinepascal/FROGS
   license: 'GNU GPL v3'
-  summary: 'FROGS is a workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data. This is the official release 2.0.0 of FROGS adapted for BIOCONDA.'
+  summary: 'FROGS is a workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data. This is the official release 3.1.0 of FROGS.'