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Update ncbi-amrfinderplus to 4.0.3 #51776

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Oct 29, 2024
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26 changes: 16 additions & 10 deletions recipes/ncbi-amrfinderplus/build.sh
Original file line number Diff line number Diff line change
@@ -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
19 changes: 12 additions & 7 deletions recipes/ncbi-amrfinderplus/meta.yaml
Original file line number Diff line number Diff line change
@@ -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:
Expand All @@ -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:
Expand All @@ -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
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