Update rgi (#11335)

* first commit * update dependencies list * change source to github * change build number * testing circleci * update meta and build * fix build * move build script into meta * remove older recipes * line fix in bootstrap.py * change python & matplotlib versions; add build.sh file * add preprocessing selector to skip python 2.7 * move build script into meta.yaml * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd.
bioconda · Oct 13, 2018 · 57ff9fb · 57ff9fb
1 parent 38217bd
commit 57ff9fb
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Showing 8 changed files with 16 additions and 194 deletions.
diff --git a/recipes/rgi/3.1.2/build.sh b/recipes/rgi/3.1.2/build.sh
diff --git a/recipes/rgi/3.1.2/meta.yaml b/recipes/rgi/3.1.2/meta.yaml
diff --git a/recipes/rgi/3.2.0/build.sh b/recipes/rgi/3.2.0/build.sh
diff --git a/recipes/rgi/3.2.0/meta.yaml b/recipes/rgi/3.2.0/meta.yaml
diff --git a/recipes/rgi/3.2.1/build.sh b/recipes/rgi/3.2.1/build.sh
diff --git a/recipes/rgi/3.2.1/meta.yaml b/recipes/rgi/3.2.1/meta.yaml
diff --git a/recipes/rgi/build.sh b/recipes/rgi/build.sh
diff --git a/recipes/rgi/meta.yaml b/recipes/rgi/meta.yaml
@@ -1,19 +1,19 @@
 {% set name = "rgi" %}
-{% set version = "4.0.3" %}
-{% set sha256 = "d82c92b2152089046fa0096f279714a068d31108030cb89c7a9fde6f9ee824b5" %}
+{% set version = "4.2.2" %}
+{% set sha256 = "ab4a5614e359884129064ec318d8dda2516052b26aa38cfd480245d24e0c96e7" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://card.mcmaster.ca/download/1/software-v{{ version }}.tar.gz
+  url: https://github.com/arpcard/rgi/archive/{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
-
 build:
-  skip: True # [win]
-  number: 3
+  skip: True # [win or py27]
+  number: 0
+  script: python setup.py install --single-version-externally-managed --record=record.txt
 
 requirements:
   build:
@@ -27,13 +27,20 @@ requirements:
   run:
     # RGI requires these exact versions of blast prodigal and diamond, or else --alignment_mode DIAMOND fails
     - python
-    - filetype
     - blast ==2.6.0
-    - biopython
     - six >=1.7.0
     - zlib
     - prodigal ==2.6.3
     - diamond ==0.8.36
+    - biopython >=1.60
+    - filetype >=1.0.0
+    - pytest >=3.0.0
+    - mock >=2.0.0
+    - pandas >=0.15.0
+    - matplotlib >=2.1.2
+    - seaborn >=0.8.1
+    - pyfaidx >=0.5.4.1
+    - pyahocorasick >=1.1.7
 
 test:
   commands:
@@ -44,11 +51,10 @@ test:
     - rgi clean -h
     - rgi galaxy -h
 
-
 about:
   home: https://card.mcmaster.ca
   license: https://card.mcmaster.ca/about
-  license_file: rgi-{{ version }}/LICENSE
+  license_file: LICENSE
   summary: 'This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website'
 
 extra: