From 57ff9fb503a7326bf6cfae7730d9949a4f754c6a Mon Sep 17 00:00:00 2001 From: mjram0s Date: Sat, 13 Oct 2018 04:00:43 -0500 Subject: [PATCH] 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 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046. --- recipes/rgi/3.1.2/build.sh | 11 -------- recipes/rgi/3.1.2/meta.yaml | 50 ---------------------------------- recipes/rgi/3.2.0/build.sh | 11 -------- recipes/rgi/3.2.0/meta.yaml | 50 ---------------------------------- recipes/rgi/3.2.1/build.sh | 3 --- recipes/rgi/3.2.1/meta.yaml | 54 ------------------------------------- recipes/rgi/build.sh | 5 ---- recipes/rgi/meta.yaml | 26 +++++++++++------- 8 files changed, 16 insertions(+), 194 deletions(-) delete mode 100644 recipes/rgi/3.1.2/build.sh delete mode 100644 recipes/rgi/3.1.2/meta.yaml delete mode 100644 recipes/rgi/3.2.0/build.sh delete mode 100644 recipes/rgi/3.2.0/meta.yaml delete mode 100644 recipes/rgi/3.2.1/build.sh delete mode 100644 recipes/rgi/3.2.1/meta.yaml delete mode 100644 recipes/rgi/build.sh diff --git a/recipes/rgi/3.1.2/build.sh b/recipes/rgi/3.1.2/build.sh deleted file mode 100644 index d70aa15af118c..0000000000000 --- a/recipes/rgi/3.1.2/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -if [ "$(uname)" == "Darwin" ]; then - echo "Platform: Mac" - -elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - echo "Platform: Linux" -fi - -# install setup -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/rgi/3.1.2/meta.yaml b/recipes/rgi/3.1.2/meta.yaml deleted file mode 100644 index a0bb75ba2a3dd..0000000000000 --- a/recipes/rgi/3.1.2/meta.yaml +++ /dev/null @@ -1,50 +0,0 @@ -{% set name = "rgi" %} -{% set version = "3.1.2" %} -{% set md5 = "272faf3ee1a3b7061f60f2c9c1c3eba7" %} -{% set commit = "8bd84b2ee5c11233992a2a8e0fb3084c76d4402c" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/arpcard/rgi_conda_dev/archive/{{ commit }}.tar.gz - md5: {{ md5 }} - -build: - skip: True # [py3k] - number: 3 - -# We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. -requirements: - build: - - {{ compiler('c') }} - host: - - python - - biopython - - six >=1.7.0 - - zlib - run: - - python - - blast - - biopython - - six >=1.7.0 - - zlib - - prodigal - - diamond >=0.8.24.86 - -test: - commands: - - rgi -h - - rgi_jsontab -h - - rgi_clean -h - - rgi_load -h - - rgi_jsonformat -h - - rgi --software_version - - rgi --data_version - -about: - home: https://card.mcmaster.ca - license: https://card.mcmaster.ca/about - 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' - diff --git a/recipes/rgi/3.2.0/build.sh b/recipes/rgi/3.2.0/build.sh deleted file mode 100644 index d70aa15af118c..0000000000000 --- a/recipes/rgi/3.2.0/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -if [ "$(uname)" == "Darwin" ]; then - echo "Platform: Mac" - -elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - echo "Platform: Linux" -fi - -# install setup -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/rgi/3.2.0/meta.yaml b/recipes/rgi/3.2.0/meta.yaml deleted file mode 100644 index 7af37f9affbd0..0000000000000 --- a/recipes/rgi/3.2.0/meta.yaml +++ /dev/null @@ -1,50 +0,0 @@ -{% set name = "rgi" %} -{% set version = "3.2.0" %} -{% set md5 = "ce60483042769072c7237427e5688ec7" %} -{% set commit = "42773177cfe0a83db9e46019c46368880a058873" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/arpcard/rgi_conda_dev/archive/{{ commit }}.tar.gz - md5: {{ md5 }} - -build: - skip: True # [py3k] - number: 3 - -# We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. -requirements: - build: - - {{ compiler('c') }} - host: - - python - - biopython - - six >=1.7.0 - - zlib - run: - - python - - blast - - biopython - - six >=1.7.0 - - zlib - - prodigal - - diamond >=0.8.24.86 - -test: - commands: - - rgi -h - - rgi_jsontab -h - - rgi_clean -h - - rgi_load -h - - rgi_jsonformat -h - - rgi --software_version - - rgi --data_version - -about: - home: https://card.mcmaster.ca - license: https://card.mcmaster.ca/about - 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' - diff --git a/recipes/rgi/3.2.1/build.sh b/recipes/rgi/3.2.1/build.sh deleted file mode 100644 index 55ea547a2d0c6..0000000000000 --- a/recipes/rgi/3.2.1/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/rgi/3.2.1/meta.yaml b/recipes/rgi/3.2.1/meta.yaml deleted file mode 100644 index e9f37b6809c96..0000000000000 --- a/recipes/rgi/3.2.1/meta.yaml +++ /dev/null @@ -1,54 +0,0 @@ -{% set name = "rgi" %} -{% set source_url = "https://github.com/arpcard/rgi_conda_dev.git" %} -{% set version = "3.2.1" %} -{% set commit = "8fa15c513f24417ba442f6bd71d3d09f80aad618" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - git_url: {{ source_url }} - git_rev: {{ commit }} - -build: - skip: True # [py3k] - number: 4 - -requirements: - build: - - {{ compiler('c') }} - host: - - python - - biopython - - six >=1.7.0 - - zlib - run: - - python - - blast - - biopython - - six >=1.7.0 - - zlib - - prodigal - - diamond >=0.8.24.86 - -test: - commands: - - rgi -h - - rgi_jsontab -h - - rgi_clean -h - - rgi_load -h - - rgi_jsonformat -h - - rgi --software_version - - rgi --data_version - -about: - home: https://card.mcmaster.ca - license: https://card.mcmaster.ca/about - summary: 'This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website' - -extra: - skip-lints: - - uses_git_url - - missing_hash - diff --git a/recipes/rgi/build.sh b/recipes/rgi/build.sh deleted file mode 100644 index 1cd853e993d97..0000000000000 --- a/recipes/rgi/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -tar xf rgi-4.0.3.tar.gz -cd rgi-4.0.3 -$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/rgi/meta.yaml b/recipes/rgi/meta.yaml index bdfd4de5f6515..e5b09d5fb0143 100644 --- 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: