Merge branch 'master' into doubletdetection

recipes/coptr/meta.yaml

@@ -13,38 +13,37 @@ build:
   entry_points:
     - coptr = coptr.cli:cli
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 1
   run_exports:
-   - {{ pin_subpackage("coptr", max_pin="x.x") }}
+   - {{ pin_subpackage("coptr", max_pin="x") }}
 
 requirements:
   host:
-    - python >=3.6
-    - setuptools >=40.6.0
-    - wheel
+    - python >=3.7
+    - setuptools
     - pip
   run:
-    - python >=3.6
+    - bowtie2 >=2.4.1
+    - python >=3.7
     - numpy >=1.19.1
     - pysam >=0.16.0.1
-    - scipy >=1.5.2
+    - scipy >=1.5.2,<2.0.0
     - matplotlib-base >=3.3.2
 
 test:
   imports:
     - coptr
   commands:
-    - pip check
     - coptr --help
-  requires:
-    - pip
 
 about:
   home: https://github.com/tyjo/coptr
   summary: Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
-  license: GPL-3.0
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: COPYING
+  dev_url: https://github.com/tyjo/coptr
 
 extra:
   recipe-maintainers:

recipes/decom/meta.yaml

@@ -2,17 +2,15 @@
 {% set version = "0.0.32" %}
 
 package:
-  name: decom
+  name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
   sha256: c9efaa97b7abfe6f19f01a199ca6c7a7b32ec699f886d226667b8b5fe562dd88
 
 build:
-  run_exports:
-    - {{ pin_subpackage('decom', max_pin="x") }}
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - decOM = decOM.__main__:main
@@ -21,24 +19,37 @@ build:
     - decOM-LOO = decOM.LOO.__main__:main
     - decOM-CV = decOM.CV.__main__:main
     - decOM-MST = decOM.MST.__main__:main
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  run_exports:
+    - {{ pin_subpackage('decom', max_pin='x.x.x') }}
 
 requirements:
   host:
     - pip
-    - python
+    - python >=3.6
+    - setuptools
   run:
+    - python >=3.6
+    - setuptools
     - colorama
+    - numpy
+    - pandas
+    - plotly >=5.5.0
     - dask >=2021.12.0
     - importlib_resources >=5.4.0
     - python-kaleido
-    - numpy >=1.7
-    - pandas
-    - plotly >=5.5.0
-    - python
     - git
 
 test:
+  imports:
+    - decOM
+    - decOM.CV
+    - decOM.LOO
+    - decOM.MST
+    - decOM.aOralOut
+    - decOM.data
+    - decOM.format
+    - decOM.modules
   commands:
     - decOM --help
     - decOM-aOralOut --help
@@ -52,9 +63,11 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: "decOM: Similarity-based microbial source tracking for contamination assessment of ancient oral samples using k-mer-based methods"
-  doc_url: "https://github.com/CamilaDuitama/decOM" 
-  dev_url: "https://camiladuitama.github.io/gradfolio/"
+  summary: "decOM: Microbial source tracking of ancient oral samples using k-mers."
+  description: |
+    decOM is a similarity-based microbial source tracking tool for contamination assessment of ancient oral samples using k-mer-based methods.
+  doc_url: https://github.com/CamilaDuitama/decOM 
+  dev_url: https://github.com/CamilaDuitama/decOM
 
 extra:
   recipe-maintainers:

recipes/deepchopper-cli/build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# -e = exit on first error
+# -x = print every executed command
+set -ex
+
+# if [ `uname` == Darwin ]; then
+#   export HOME=`mktemp -d`
+# fi
+
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y
+
+export PATH="$HOME/.cargo/bin:$PATH"
+
+cd py_cli
+
+maturin build --interpreter python --release -b bin --out dist
+
+$PYTHON -m pip install dist/*.whl --no-deps --ignore-installed -vv

recipes/deepchopper-cli/meta.yaml

@@ -0,0 +1,56 @@
+{% set name = "deepchopper-cli" %}
+{% set version = "1.2.5" %}
+{% set sha256 = "fc5ceaf204f82eeae1b82488ee44d020c66b0df13d27a86658ed86a7b1774dbb" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepchopper_cli-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [py < 310]
+  run_exports:
+    - {{ pin_subpackage("deepchopper-cli", max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('c') }}
+    - make
+    - cmake
+  host:
+    - python
+    - pip
+    - maturin >=1.2.1,<2
+    - setuptools-rust
+    - setuptools
+  run:
+    - python
+
+
+test:
+  commands:
+    - deepchopper-chop -h
+
+about:
+  home: https://github.com/ylab-hi/DeepChopper
+  license: Apache-2.0
+  license_family: Apache
+  license_file: LICENSE
+  summary: 'A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.'
+  description: |
+    DeepChopper is a genomic language model designed to identify artificial sequences.
+    It provides functionality for encoding FASTQ files, making predictions, and chopping sequences.
+  doc_url: https://github.com/ylab-hi/DeepChopper
+  dev_url: https://github.com/ylab-hi/DeepChopper
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - yangyangli

recipes/geosketch/meta.yaml

@@ -1,18 +1,20 @@
 {% set name = "geosketch" %}
-{% set version = "1.2" %}
+{% set version = "1.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e
+  sha256: 2b2a6056c2134048fa85972ee93b95bdf53555fdf482cc4bfc29c485b78bb5f4
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed -vv ."
+  script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv ."
+  run_exports:
+    - {{ pin_subpackage('geosketch', max_pin="x") }}
 
 requirements:
   host:
@@ -30,9 +32,10 @@ test:
     - geosketch
 
 about:
-  home: https://github.com/brianhie/geosketch/
+  home: https://github.com/brianhie/geosketch
   license: MIT
-  summary: Geometry-preserving random sampling
+  license_family: MIT
+  summary: "Geometry-preserving random sampling."
 
 extra:
   identifiers:

recipes/jarvis3/build.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include
+export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
+
+cd src 
+make CC=$CC CFLAGS="$CFLAGS -fcommon"
+mkdir -p ${PREFIX}/bin
+make
+
+mv extra/ ${PREFIX}/bin
+mv JARVIS3.sh ${PREFIX}/bin
+mv JARVIS3 ${PREFIX}/bin
+
+cd ${PREFIX}/bin
+sed -i.bak 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh
+rm JARVIS3.sh
+mv aux.sh JARVIS3.sh
+chmod +x JARVIS3.sh
+JARVIS3.sh --install

recipes/jarvis3/meta.yaml

@@ -0,0 +1,34 @@
+{% set version = "3.7" %}
+
+package:
+  name: jarvis3
+  version: {{ version }}
+
+build:
+  # Passes some invalid flags for clang
+  skip: True  # [osx]
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("jarvis3", max_pin="x") }}
+
+source:
+  url: https://github.com/cobilab/jarvis3/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 7600b4da05d27150e96f3481ca5e8cbc1dc75ee1b537727abf717224ed42c613
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+
+test:
+  commands:
+    - JARVIS3 --version 2>&1 | grep "Version 3, Release 7"
+    #- printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa; JARVIS3.sh -i test.fa | grep "test.fa.tar"
+
+about:
+  home: https://github.com/cobilab/jarvis3
+  license: GPL3
+  license_file: LICENSE
+  license_family: GPL3
+  summary: Improved encoder for genomic sequences.
+  dev_url: https://github.com/cobilab/jarvis3

recipes/ncbi-amrfinderplus/build.sh

@@ -1,21 +1,27 @@
 #!/bin/bash
 
 echo "DEBUGGING environment info because PREFIX did not appear to be set"
-echo "PREFIX=$PREFIX    CONDA_PREFIX=$CONDA_PREFIX"
+echo "PREFIX=$PREFIX CONDA_PREFIX=$CONDA_PREFIX"
 echo "PREFIX =" $PREFIX CONDA_PREFIX = $CONDA_PREFIX BUILD_PREFIX = $BUILD_PREFIX
 echo $PREFIX
 
-# test fix for version 3.9.8
-# move patch to meta.yaml
-# patch < patch.3.9.8
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
 # fix error because of gnu++17 features. Suggested by https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
-CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
 
-# note that for version 3.7 the make command should be:
-make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX="$PREFIX" CONDA_DB_DIR="$CONDA_PREFIX/share/amrfinderplus/data"
+# Get StxTyper source as well
+git submodule update --init
 
-#echo "make CXX=\"$CXX $LDFLAGS\" CPPFLAGS=\"$CXXFLAGS\" PREFIX=\"$PREFIX\" DEFAULT_DB_DIR=\"$PREFIX/share/amrfinderplus/data\""
+make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS -I${PREFIX}/include" PREFIX="$PREFIX" DEFAULT_DB_DIR="${PREFIX}/share/amrfinderplus/data" -j"${CPU_COUNT}"
 
-#make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX=$PREFIX DEFAULT_DB_DIR="$PREFIX/share/amrfinderplus/data"
-make install bindir=$PREFIX/bin
+make install INSTALL_DIR="$PREFIX/bin"
+
+### Temporary bug fix for issue with Makefile. These lines have been added to the makefile
+# for future releases, so remove after version 4.0.3
+if [ ! -e "$PREFIX/bin/stx/stxtyper" ]
+then
+    mkdir "$PREFIX/bin/stx"
+    ln -s ../stxtyper "$PREFIX/bin/stx/stxtyper"
+fi
+# end bug fix

recipes/ncbi-amrfinderplus/meta.yaml

@@ -1,12 +1,13 @@
-{% set version = "3.12.8" %}
-{% set sha256 = "a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0" %}
+{% set version = "4.0.3" %}
+{% set sha256 = "e3007c074ac77e410914691b38d7eaaaaf2cda6c" %}
 
 package:
   name: ncbi-amrfinderplus
   version: {{ version }}
 
 source:
-  url: https://github.com/ncbi/amr/archive/amrfinder_v{{ version }}.tar.gz
+  git_url: https://github.com/ncbi/amr.git
+  git_rev: amrfinder_v{{ version }}
   sha256: {{ sha256 }}
 
 build:
@@ -16,15 +17,15 @@ build:
 
 requirements:
   build:
+    - git
     - make
     - {{ compiler('cxx') }}
-  host:
     - coreutils
+  host:
     - libcurl
   run:
     - blast >=2.9
     - hmmer >=3.2
-    - libcurl
     - curl
 
 test:
@@ -47,20 +48,24 @@ test:
         diff test_both.expected test_both.got
 
 about:
-  home: https://github.com/ncbi/amr/wiki
+  home: https://github.com/ncbi/amr
   license: Public Domain
   license_file: LICENSE
-  summary: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
+  summary: "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences."
   description: |
       This software and the accompanying database are designed to
       find acquired antimicrobial resistance genes in bacterial protein or
       nucleotide sequences as well as known point mutations for several taxa. With
       AMRFinderPlus we have added select members of additional classes of genes
       such as virulence factors, biocide, heat, acid, and metal resistance genes.
   doc_url: https://github.com/ncbi/amr/wiki
+  dev_url: https://github.com/ncbi/amr
 
 extra:
   recipe-maintainers:
     - evolarjun
   identifiers:
     - doi:10.1038/s41598-021-91456-0
+  skip-lints:
+    - uses_vcs_url
+    - missing_hash