From a75ce87420fff0e153998160b3ac30499c7993c6 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 16:10:22 +0000
Subject: [PATCH 1/8] Update ncbi-amrfinderplus to 4.0.3

---
 recipes/ncbi-amrfinderplus/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index 1e8066c9c665a..c171b2c3ae577 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "3.12.8" %}
-{% set sha256 = "a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0" %}
+{% set version = "4.0.3" %}
+{% set sha256 = "80ad1e217c78024633aa6e11052f6290b445414251372e4379c373915768564d" %}
 
 package:
   name: ncbi-amrfinderplus

From 22d91be51726daf9b8bbfa00527ea3070613340e Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Tue, 29 Oct 2024 15:30:46 -0400
Subject: [PATCH 2/8] Try switching to git for checkout

We need to enable the submodule so I'm going to try using git for checkout.
---
 recipes/ncbi-amrfinderplus/meta.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index c171b2c3ae577..478d520016c85 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -6,16 +6,19 @@ package:
   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: {{ version }}
   sha256: {{ sha256 }}
+  git_depth: 10
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('ncbi-amrfinderplus', max_pin="x") }}
 
 requirements:
   build:
+    - git
     - make
     - {{ compiler('cxx') }}
   host:

From 67f4b31c13e36394d582bb609275130cde1e1976 Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Tue, 29 Oct 2024 15:31:44 -0400
Subject: [PATCH 3/8] Add git submodule update --init

---
 recipes/ncbi-amrfinderplus/build.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/recipes/ncbi-amrfinderplus/build.sh b/recipes/ncbi-amrfinderplus/build.sh
index 67becc82bc7d9..68bec62e7f64f 100755
--- a/recipes/ncbi-amrfinderplus/build.sh
+++ b/recipes/ncbi-amrfinderplus/build.sh
@@ -12,6 +12,9 @@ echo $PREFIX
 # fix error because of gnu++17 features. Suggested by https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
 CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
 
+# Get StxTyper source as well
+git submodule update --init
+
 # 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"
 

From 76a0736d4d0f45a6818d1c2c5b8f98286555f749 Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Tue, 29 Oct 2024 15:42:20 -0400
Subject: [PATCH 4/8] Reset build number to zero and remove sha hash

---
 recipes/ncbi-amrfinderplus/meta.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index 478d520016c85..1bfa78798e338 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -8,11 +8,10 @@ package:
 source:
   git_url: https://github.com/ncbi/amr.git
   git_rev: {{ version }}
-  sha256: {{ sha256 }}
   git_depth: 10
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('ncbi-amrfinderplus', max_pin="x") }}
 

From dad461763bcb7507477e7cadd24a4b5009610421 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 29 Oct 2024 14:52:33 -0500
Subject: [PATCH 5/8] add skip-lints

---
 recipes/ncbi-amrfinderplus/meta.yaml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index 1bfa78798e338..e94af7ec70c20 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -7,8 +7,7 @@ package:
 
 source:
   git_url: https://github.com/ncbi/amr.git
-  git_rev: {{ version }}
-  git_depth: 10
+  git_rev: amrfinder_v{{ version }}
 
 build:
   number: 0
@@ -20,13 +19,12 @@ requirements:
     - git
     - make
     - {{ compiler('cxx') }}
-  host:
     - coreutils
+  host:
     - libcurl
   run:
     - blast >=2.9
     - hmmer >=3.2
-    - libcurl
     - curl
 
 test:
@@ -49,10 +47,10 @@ 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
@@ -60,9 +58,13 @@ about:
       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

From 908a96300f44ee78c8c31ab7e172930a9493a1b1 Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Tue, 29 Oct 2024 16:00:15 -0400
Subject: [PATCH 6/8] Add sha256 back into the source clause

---
 recipes/ncbi-amrfinderplus/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index e94af7ec70c20..3ee0696cc7bec 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -1,5 +1,5 @@
 {% set version = "4.0.3" %}
-{% set sha256 = "80ad1e217c78024633aa6e11052f6290b445414251372e4379c373915768564d" %}
+{% set sha256 = "e3007c074ac77e410914691b38d7eaaaaf2cda6c" %}
 
 package:
   name: ncbi-amrfinderplus
@@ -8,6 +8,7 @@ package:
 source:
   git_url: https://github.com/ncbi/amr.git
   git_rev: amrfinder_v{{ version }}
+  sha256: {{ sha256 }}
 
 build:
   number: 0

From 91766e3aaa2b35e913fcc26e17c90dedb72c249d Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 29 Oct 2024 15:55:23 -0500
Subject: [PATCH 7/8] edit build.sh

---
 recipes/ncbi-amrfinderplus/build.sh | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/recipes/ncbi-amrfinderplus/build.sh b/recipes/ncbi-amrfinderplus/build.sh
index 68bec62e7f64f..a70a91028df44 100755
--- a/recipes/ncbi-amrfinderplus/build.sh
+++ b/recipes/ncbi-amrfinderplus/build.sh
@@ -1,24 +1,18 @@
 #!/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"
 
 # Get StxTyper source as well
 git submodule update --init
 
-# 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"
+make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS -I${PREFIX}/include" PREFIX="$PREFIX" DEFAULT_DB_DIR="${PREFIX}/share/amrfinderplus/data" -j"${CPU_COUNT}"
 
-#echo "make CXX=\"$CXX $LDFLAGS\" CPPFLAGS=\"$CXXFLAGS\" PREFIX=\"$PREFIX\" DEFAULT_DB_DIR=\"$PREFIX/share/amrfinderplus/data\""
-
-#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"

From 751cd3e11c71126449a23d64ae763e9121d9b067 Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Tue, 29 Oct 2024 17:01:45 -0400
Subject: [PATCH 8/8] Fix for Makefile install target bug

---
 recipes/ncbi-amrfinderplus/build.sh | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/recipes/ncbi-amrfinderplus/build.sh b/recipes/ncbi-amrfinderplus/build.sh
index a70a91028df44..417e5c7226118 100755
--- a/recipes/ncbi-amrfinderplus/build.sh
+++ b/recipes/ncbi-amrfinderplus/build.sh
@@ -16,3 +16,12 @@ git submodule update --init
 make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS -I${PREFIX}/include" PREFIX="$PREFIX" DEFAULT_DB_DIR="${PREFIX}/share/amrfinderplus/data" -j"${CPU_COUNT}"
 
 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