From f8740fe8927ed0247bbce0cddb609f64c56aa7b4 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Tue, 18 Mar 2025 14:53:19 +0800
Subject: [PATCH 01/15] linux-aarch64 build for nrpys python <312

---
 recipes/nrpys/meta.yaml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml
index e1a1b94498112..4b042b97f3d08 100644
--- a/recipes/nrpys/meta.yaml
+++ b/recipes/nrpys/meta.yaml
@@ -7,8 +7,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 3
-  noarch: python
+  number: 5
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -20,14 +19,16 @@ source:
     - pyproject.patch
 
 requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('rust') }}
   host:
-    - python >=3.8
+    - python <3.12
     - pip
-    - rust
     - maturin
     - zlib
   run:
-    - python >=3.8
+    - python <3.12
 
 test:
   imports:
@@ -38,3 +39,7 @@ about:
   license: AGPL-3.0-or-later
   license_file: LICENSE.txt
   summary: "Python language bindings for nrps-rs substrate specificity predictor."
+
+extra:
+  additional-platforms:
+    - linux-aarch64

From 7e90b21020496cbf386e588cef6f1a272d875612 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Tue, 18 Mar 2025 14:54:07 +0800
Subject: [PATCH 02/15] Revert "linux-aarch64 build for nrpys python <312"

This reverts commit f8740fe8927ed0247bbce0cddb609f64c56aa7b4.
---
 recipes/nrpys/meta.yaml | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml
index 4b042b97f3d08..e1a1b94498112 100644
--- a/recipes/nrpys/meta.yaml
+++ b/recipes/nrpys/meta.yaml
@@ -7,7 +7,8 @@ package:
   version: {{ version }}
 
 build:
-  number: 5
+  number: 3
+  noarch: python
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -19,16 +20,14 @@ source:
     - pyproject.patch
 
 requirements:
-  build:
-    - {{ compiler('c') }}
-    - {{ compiler('rust') }}
   host:
-    - python <3.12
+    - python >=3.8
     - pip
+    - rust
     - maturin
     - zlib
   run:
-    - python <3.12
+    - python >=3.8
 
 test:
   imports:
@@ -39,7 +38,3 @@ about:
   license: AGPL-3.0-or-later
   license_file: LICENSE.txt
   summary: "Python language bindings for nrps-rs substrate specificity predictor."
-
-extra:
-  additional-platforms:
-    - linux-aarch64

From 4e359dffd52323df4088466dd8f3c9176c4fd2de Mon Sep 17 00:00:00 2001
From: ZerryNi <996002763.com>
Date: Wed, 14 May 2025 20:35:12 +0800
Subject: [PATCH 03/15] linux-aarch64 build for humann2

---
 recipes/humann2/build.sh  |  5 +++
 recipes/humann2/meta.yaml | 88 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 recipes/humann2/build.sh
 create mode 100644 recipes/humann2/meta.yaml

diff --git a/recipes/humann2/build.sh b/recipes/humann2/build.sh
new file mode 100644
index 0000000000000..7da76de21b8d3
--- /dev/null
+++ b/recipes/humann2/build.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+$PYTHON setup.py install \
+    --bypass-dependencies-install \
+    --single-version-externally-managed --record=record.txt
diff --git a/recipes/humann2/meta.yaml b/recipes/humann2/meta.yaml
new file mode 100644
index 0000000000000..13aa067759716
--- /dev/null
+++ b/recipes/humann2/meta.yaml
@@ -0,0 +1,88 @@
+package:
+  name: humann2
+  version: "2.8.1"
+
+build:
+  number: 1
+  run_exports: # run_exports这个要配置上, 不然提交可能check不通过
+    - {{ pin_subpackage('humann2', max_pin="x.x") }}
+  skip: false # [not py27 and not py34]
+  noarch: python
+  entry_points:
+    - humann2 = humann2.humann2:main
+    - humann2_databases = humann2.tools.humann2_databases:main
+    - humann2_config = humann2.tools.humann2_config:main
+    - humann2_join_tables = humann2.tools.join_tables:main
+    - humann2_split_table = humann2.tools.split_table:main
+    - humann2_rename_table = humann2.tools.rename_table:main
+    - humann2_renorm_table = humann2.tools.renorm_table:main
+    - humann2_regroup_table = humann2.tools.regroup_table:main
+    - humann2_infer_taxonomy = humann2.tools.infer_taxonomy:main
+    - humann2_humann1_kegg = humann2.tools.humann2_humann1_kegg:main
+    - humann2_rna_dna_norm = humann2.tools.rna_dna_norm:main
+    - humann2_strain_profiler = humann2.tools.strain_profiler:main
+    - humann2_reduce_table = humann2.tools.reduce_table:main
+    - humann2_unpack_pathways = humann2.tools.merge_abundance:main
+    - humann2_test = humann2.tests.humann2_test:main
+    - humann2_build_custom_database = humann2.tools.build_custom_database:main
+    - humann2_genefamilies_genus_level = humann2.tools.genefamilies_genus_level:main
+    - humann2_split_stratified_table = humann2.tools.split_stratified_table:main
+    - humann2_associate = humann2.tools.humann2_associate:main
+    - humann2_barplot = humann2.tools.humann2_barplot:main
+    - humann2_benchmark = humann2.tools.humann2_benchmark:main
+
+source:
+  url: https://files.pythonhosted.org/packages/eb/b4/c6975eb023e915ef999184c040474a781c3f0979d2f1c557fc6e693a7dbb/humann2-2.8.1.tar.gz
+  sha256: 1b2e646eea8de21c8ccc3bbb128e8aa57bf7e8f9901c3098cb6a0eeb10a82489
+
+requirements:
+  host:
+    - python
+    - setuptools
+  run:
+    - python >=3.12
+    - bowtie2 >=2.2.5
+    - metaphlan2 >=2.6.0
+    - diamond >=0.7.10,<0.9.0
+    - samtools
+    - biom-format
+    - matplotlib-base
+    - scipy
+    - numpy
+
+test:
+  imports:
+    - humann2
+    - humann2.quantify
+    - humann2.search
+    - humann2.tests
+    - humann2.tools
+  commands:
+    - humann2 --help
+    - humann2_databases --help
+    - humann2_config --help
+    - humann2_join_tables --help
+    - humann2_split_table --help
+    - humann2_rename_table --help
+    - humann2_renorm_table --help
+    - humann2_regroup_table --help
+    - humann2_infer_taxonomy --help 2>&1 | grep "HUMAnN2"
+    - humann2_humann1_kegg --help
+    - humann2_rna_dna_norm --help
+    - humann2_strain_profiler --help
+    - humann2_reduce_table --help
+    - humann2_unpack_pathways --help
+    - humann2_test --help
+    - humann2_build_custom_database --help
+    - humann2_genefamilies_genus_level --help
+    - humann2_split_stratified_table --help
+    - humann2_associate --help
+    - humann2_barplot --help
+    - humann2_benchmark --help
+
+about:
+  home: http://huttenhower.sph.harvard.edu/humann2
+  license: MIT
+  summary: 'HUMAnN2: The HMP Unified Metabolic Analysis Network 2'
+  license_family: MIT
+

From 5d901e14186370f7f5cbac2fb9cc0d550cb74732 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Mon, 9 Jun 2025 19:55:36 +0800
Subject: [PATCH 04/15] update humman2

---
 recipes/humann2/build.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/recipes/humann2/build.sh b/recipes/humann2/build.sh
index 7da76de21b8d3..3786386a73c83 100644
--- a/recipes/humann2/build.sh
+++ b/recipes/humann2/build.sh
@@ -1,5 +1,3 @@
 #!/bin/bash
 
-$PYTHON setup.py install \
-    --bypass-dependencies-install \
-    --single-version-externally-managed --record=record.txt
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt

From d502af5a6fb67bb0eb26ddf344ec77958f64e498 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Tue, 10 Jun 2025 10:03:01 +0800
Subject: [PATCH 05/15] update origin

---
 recipes/humann2/build.sh  |  3 --
 recipes/humann2/meta.yaml | 88 ---------------------------------------
 2 files changed, 91 deletions(-)
 delete mode 100644 recipes/humann2/build.sh
 delete mode 100644 recipes/humann2/meta.yaml

diff --git a/recipes/humann2/build.sh b/recipes/humann2/build.sh
deleted file mode 100644
index 3786386a73c83..0000000000000
--- a/recipes/humann2/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
diff --git a/recipes/humann2/meta.yaml b/recipes/humann2/meta.yaml
deleted file mode 100644
index 13aa067759716..0000000000000
--- a/recipes/humann2/meta.yaml
+++ /dev/null
@@ -1,88 +0,0 @@
-package:
-  name: humann2
-  version: "2.8.1"
-
-build:
-  number: 1
-  run_exports: # run_exports这个要配置上, 不然提交可能check不通过
-    - {{ pin_subpackage('humann2', max_pin="x.x") }}
-  skip: false # [not py27 and not py34]
-  noarch: python
-  entry_points:
-    - humann2 = humann2.humann2:main
-    - humann2_databases = humann2.tools.humann2_databases:main
-    - humann2_config = humann2.tools.humann2_config:main
-    - humann2_join_tables = humann2.tools.join_tables:main
-    - humann2_split_table = humann2.tools.split_table:main
-    - humann2_rename_table = humann2.tools.rename_table:main
-    - humann2_renorm_table = humann2.tools.renorm_table:main
-    - humann2_regroup_table = humann2.tools.regroup_table:main
-    - humann2_infer_taxonomy = humann2.tools.infer_taxonomy:main
-    - humann2_humann1_kegg = humann2.tools.humann2_humann1_kegg:main
-    - humann2_rna_dna_norm = humann2.tools.rna_dna_norm:main
-    - humann2_strain_profiler = humann2.tools.strain_profiler:main
-    - humann2_reduce_table = humann2.tools.reduce_table:main
-    - humann2_unpack_pathways = humann2.tools.merge_abundance:main
-    - humann2_test = humann2.tests.humann2_test:main
-    - humann2_build_custom_database = humann2.tools.build_custom_database:main
-    - humann2_genefamilies_genus_level = humann2.tools.genefamilies_genus_level:main
-    - humann2_split_stratified_table = humann2.tools.split_stratified_table:main
-    - humann2_associate = humann2.tools.humann2_associate:main
-    - humann2_barplot = humann2.tools.humann2_barplot:main
-    - humann2_benchmark = humann2.tools.humann2_benchmark:main
-
-source:
-  url: https://files.pythonhosted.org/packages/eb/b4/c6975eb023e915ef999184c040474a781c3f0979d2f1c557fc6e693a7dbb/humann2-2.8.1.tar.gz
-  sha256: 1b2e646eea8de21c8ccc3bbb128e8aa57bf7e8f9901c3098cb6a0eeb10a82489
-
-requirements:
-  host:
-    - python
-    - setuptools
-  run:
-    - python >=3.12
-    - bowtie2 >=2.2.5
-    - metaphlan2 >=2.6.0
-    - diamond >=0.7.10,<0.9.0
-    - samtools
-    - biom-format
-    - matplotlib-base
-    - scipy
-    - numpy
-
-test:
-  imports:
-    - humann2
-    - humann2.quantify
-    - humann2.search
-    - humann2.tests
-    - humann2.tools
-  commands:
-    - humann2 --help
-    - humann2_databases --help
-    - humann2_config --help
-    - humann2_join_tables --help
-    - humann2_split_table --help
-    - humann2_rename_table --help
-    - humann2_renorm_table --help
-    - humann2_regroup_table --help
-    - humann2_infer_taxonomy --help 2>&1 | grep "HUMAnN2"
-    - humann2_humann1_kegg --help
-    - humann2_rna_dna_norm --help
-    - humann2_strain_profiler --help
-    - humann2_reduce_table --help
-    - humann2_unpack_pathways --help
-    - humann2_test --help
-    - humann2_build_custom_database --help
-    - humann2_genefamilies_genus_level --help
-    - humann2_split_stratified_table --help
-    - humann2_associate --help
-    - humann2_barplot --help
-    - humann2_benchmark --help
-
-about:
-  home: http://huttenhower.sph.harvard.edu/humann2
-  license: MIT
-  summary: 'HUMAnN2: The HMP Unified Metabolic Analysis Network 2'
-  license_family: MIT
-

From 1de2cf022574d2aca62a461f13db193cf9f77f8f Mon Sep 17 00:00:00 2001
From: cfmin09 <1163105507@qq.com>
Date: Wed, 11 Jun 2025 14:51:07 +0800
Subject: [PATCH 06/15] Update rascaf and enabled aarch64

---
 recipes/rascaf/build.sh  |  8 ++++++++
 recipes/rascaf/meta.yaml | 11 ++++++-----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/recipes/rascaf/build.sh b/recipes/rascaf/build.sh
index 14c590bcd40d4..a80a14b033453 100755
--- a/recipes/rascaf/build.sh
+++ b/recipes/rascaf/build.sh
@@ -1,4 +1,12 @@
 #!/bin/bash
+
+sed -i '/char nucToNum/s/^/signed\ /g' defs.h
+sed -i '/char numToNuc/s/^/signed\ /g' defs.h
+sed -i 's/extern char nucToNum/extern signed char nucToNum/g' KmerCode.hpp
+sed -i 's/extern char numToNuc/extern signed char numToNuc/g' KmerCode.hpp
+sed -i 's/extern char nucToNum/extern signed char nucToNum/g' genome.hpp
+sed -i 's/extern char numToNuc/extern signed char numToNuc/g' genome.hpp
+
 make \
     CXX="${CXX}" \
     CXXFLAGS="${CXXFLAGS} -Wformat -O3" \
diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index eeace467d33c6..9be6ef6e78afc 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "20161129" %}
+{% set version = "20180710" %}
 
 package:
   name: rascaf
@@ -7,11 +7,13 @@ package:
 build:
   # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
   skip: True  # [osx]
-  number: 7
+  number: 8
+  run_exports:
+    - {{ pin_subpackage(name|lower) }}
 
 source:
-  url: https://github.com/mourisl/Rascaf/archive/ed779e100853977307bbdc01c1644390d8556a7b.tar.gz
-  md5: b05116262162712098b357871f1a79e4
+  url: https://github.com/mourisl/Rascaf/archive/690f618e59b1f555fafa406ad1b6b95c1b0423b4.tar.gz
+  md5: 7478d8db1e4f5618ee9ab0dfae23815f
   patches:
     - 0001-Unvendor-samtools.patch
 
@@ -35,4 +37,3 @@ about:
   home: https://github.com/mourisl/Rascaf/commits/master
   summary: Scaffolding with RNA-seq read alignment
   license: GPL2
-

From 710879283ebda1fd2ea2ccbdefd6ce92f6d6d917 Mon Sep 17 00:00:00 2001
From: ZerryNi <47553636+ZerryNi@users.noreply.github.com>
Date: Thu, 12 Jun 2025 10:37:19 +0800
Subject: [PATCH 07/15] Update meta.yaml

---
 recipes/rascaf/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index 9be6ef6e78afc..ed46b5205475d 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -7,7 +7,7 @@ package:
 build:
   # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
   skip: True  # [osx]
-  number: 8
+  number: 0
   run_exports:
     - {{ pin_subpackage(name|lower) }}
 

From d93cc58410eb9345f08ee8a678801cc56581ce10 Mon Sep 17 00:00:00 2001
From: ZerryNi <47553636+ZerryNi@users.noreply.github.com>
Date: Thu, 12 Jun 2025 10:48:20 +0800
Subject: [PATCH 08/15] Update meta.yaml

---
 recipes/rascaf/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index ed46b5205475d..a1564ff6a4908 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -1,3 +1,4 @@
+{% set name = "rascaf" %}
 {% set version = "20180710" %}
 
 package:

From c590cfc7dc6cc615812760b4d30097d456928cb6 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:00:59 -0500
Subject: [PATCH 09/15] Update meta.yaml

---
 recipes/rascaf/meta.yaml | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index a1564ff6a4908..e79d2c6ab86dc 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -2,22 +2,21 @@
 {% set version = "20180710" %}
 
 package:
-  name: rascaf
+  name: {{ name }}
   version: {{ version }}
 
-build:
-  # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
-  skip: True  # [osx]
-  number: 0
-  run_exports:
-    - {{ pin_subpackage(name|lower) }}
-
 source:
   url: https://github.com/mourisl/Rascaf/archive/690f618e59b1f555fafa406ad1b6b95c1b0423b4.tar.gz
   md5: 7478d8db1e4f5618ee9ab0dfae23815f
   patches:
     - 0001-Unvendor-samtools.patch
 
+build:
+  # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower) }}
+
 requirements:
   build:
     - make
@@ -26,8 +25,6 @@ requirements:
   host:
     - samtools 0.1.19.*
     - zlib
-  run:
-    - zlib
 
 test:
   commands:
@@ -35,6 +32,16 @@ test:
     - rascaf-join 2>&1 | grep usage > /dev/null
 
 about:
-  home: https://github.com/mourisl/Rascaf/commits/master
-  summary: Scaffolding with RNA-seq read alignment
-  license: GPL2
+  home: "https://github.com/mourisl/Rascaf"
+  summary: "Scaffolding with RNA-seq read alignment."
+  license: "GPL-2.0-or-later"
+  license_family: GPL
+  dev_url: "https://github.com/mourisl/Rascaf"
+  doc_url: "https://github.com/mourisl/Rascaf/blob/v{{ version }}/README.md"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - doi:10.3835/plantgenome2016.03.0027

From 0af33255f6eec345b9504220b40498497a2d1cfa Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:04:15 -0500
Subject: [PATCH 10/15] Update build.sh

---
 recipes/rascaf/build.sh | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/recipes/rascaf/build.sh b/recipes/rascaf/build.sh
index a80a14b033453..e8bf5eff33176 100755
--- a/recipes/rascaf/build.sh
+++ b/recipes/rascaf/build.sh
@@ -1,19 +1,24 @@
 #!/bin/bash
 
-sed -i '/char nucToNum/s/^/signed\ /g' defs.h
-sed -i '/char numToNuc/s/^/signed\ /g' defs.h
-sed -i 's/extern char nucToNum/extern signed char nucToNum/g' KmerCode.hpp
-sed -i 's/extern char numToNuc/extern signed char numToNuc/g' KmerCode.hpp
-sed -i 's/extern char nucToNum/extern signed char nucToNum/g' genome.hpp
-sed -i 's/extern char numToNuc/extern signed char numToNuc/g' genome.hpp
+export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal"
 
-make \
-    CXX="${CXX}" \
-    CXXFLAGS="${CXXFLAGS} -Wformat -O3" \
-    LINKPATH="${LDFLAGS}"
-install -d "${PREFIX}/bin"
-install \
+mkdir -p "${PREFIX}/bin"
+
+sed -i.bak '/char nucToNum/s/^/signed\ /g' defs.h
+sed -i.bak '/char numToNuc/s/^/signed\ /g' defs.h
+sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' KmerCode.hpp
+sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' KmerCode.hpp
+sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' genome.hpp
+sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' genome.hpp
+
+make CXX="${CXX}" \
+    CXXFLAGS="${CXXFLAGS}" LINKPATH="${LDFLAGS}" \
+    -j"${CPU_COUNT}"
+
+install -v -m 755 \
     *.pl \
     rascaf \
     rascaf-join \
-    "${PREFIX}/bin/"
+    "${PREFIX}/bin"

From 91bc06d982a1a87288728864c3fe77d132f91f83 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:28:08 -0500
Subject: [PATCH 11/15] Update build.sh

---
 recipes/rascaf/build.sh | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/recipes/rascaf/build.sh b/recipes/rascaf/build.sh
index e8bf5eff33176..0f46375f67f66 100755
--- a/recipes/rascaf/build.sh
+++ b/recipes/rascaf/build.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
 
+mkdir -p "${PREFIX}/bin"
+
 export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal"
-
-mkdir -p "${PREFIX}/bin"
+export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal -Wno-writable-strings -Wno-literal-suffix"
 
 sed -i.bak '/char nucToNum/s/^/signed\ /g' defs.h
 sed -i.bak '/char numToNuc/s/^/signed\ /g' defs.h
@@ -12,6 +12,11 @@ sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' KmerCode.hpp
 sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' KmerCode.hpp
 sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' genome.hpp
 sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' genome.hpp
+sed -i.bak 's/-lpthread/-pthread/g' Makefile
+
+# Fix perl shebang
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' *.pl
+rm -rf *.bak
 
 make CXX="${CXX}" \
     CXXFLAGS="${CXXFLAGS}" LINKPATH="${LDFLAGS}" \

From 05f74bdbf3ba3bd4f86f4ca3ef4d250c78be6b93 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:39:58 -0500
Subject: [PATCH 12/15] Update build.sh

---
 recipes/rascaf/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/rascaf/build.sh b/recipes/rascaf/build.sh
index 0f46375f67f66..a9cd1f55a3a70 100755
--- a/recipes/rascaf/build.sh
+++ b/recipes/rascaf/build.sh
@@ -2,9 +2,9 @@
 
 mkdir -p "${PREFIX}/bin"
 
-export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
+export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include -Wno-writable-strings -Wno-literal-suffix"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal -Wno-writable-strings -Wno-literal-suffix"
+export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal"
 
 sed -i.bak '/char nucToNum/s/^/signed\ /g' defs.h
 sed -i.bak '/char numToNuc/s/^/signed\ /g' defs.h

From af75cb558490feb2cf62a9a8160d8a178ffebd5c Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:42:31 -0500
Subject: [PATCH 13/15] samtools 0.1.19 does not have osx-arm64; disable
 osx-arm64

---
 recipes/rascaf/meta.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index e79d2c6ab86dc..525debc898b65 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -12,10 +12,9 @@ source:
     - 0001-Unvendor-samtools.patch
 
 build:
-  # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
   number: 0
   run_exports:
-    - {{ pin_subpackage(name|lower) }}
+    - {{ pin_subpackage('rascaf', max_pin=None) }}
 
 requirements:
   build:
@@ -42,6 +41,5 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
-    - osx-arm64
   identifiers:
     - doi:10.3835/plantgenome2016.03.0027

From 7a4fd3f283e78d2914691040818227743155671b Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 12 Jun 2025 16:43:47 -0500
Subject: [PATCH 14/15] Update meta.yaml

---
 recipes/rascaf/build.sh  | 32 +++++++-------------------------
 recipes/rascaf/meta.yaml |  2 +-
 2 files changed, 8 insertions(+), 26 deletions(-)

diff --git a/recipes/rascaf/build.sh b/recipes/rascaf/build.sh
index a9cd1f55a3a70..14c590bcd40d4 100755
--- a/recipes/rascaf/build.sh
+++ b/recipes/rascaf/build.sh
@@ -1,29 +1,11 @@
 #!/bin/bash
-
-mkdir -p "${PREFIX}/bin"
-
-export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include -Wno-writable-strings -Wno-literal-suffix"
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -Wformat -Wno-reserved-user-defined-literal"
-
-sed -i.bak '/char nucToNum/s/^/signed\ /g' defs.h
-sed -i.bak '/char numToNuc/s/^/signed\ /g' defs.h
-sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' KmerCode.hpp
-sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' KmerCode.hpp
-sed -i.bak 's/extern char nucToNum/extern signed char nucToNum/g' genome.hpp
-sed -i.bak 's/extern char numToNuc/extern signed char numToNuc/g' genome.hpp
-sed -i.bak 's/-lpthread/-pthread/g' Makefile
-
-# Fix perl shebang
-sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' *.pl
-rm -rf *.bak
-
-make CXX="${CXX}" \
-    CXXFLAGS="${CXXFLAGS}" LINKPATH="${LDFLAGS}" \
-    -j"${CPU_COUNT}"
-
-install -v -m 755 \
+make \
+    CXX="${CXX}" \
+    CXXFLAGS="${CXXFLAGS} -Wformat -O3" \
+    LINKPATH="${LDFLAGS}"
+install -d "${PREFIX}/bin"
+install \
     *.pl \
     rascaf \
     rascaf-join \
-    "${PREFIX}/bin"
+    "${PREFIX}/bin/"
diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml
index 525debc898b65..d60c0cbbcc96c 100644
--- a/recipes/rascaf/meta.yaml
+++ b/recipes/rascaf/meta.yaml
@@ -36,7 +36,7 @@ about:
   license: "GPL-2.0-or-later"
   license_family: GPL
   dev_url: "https://github.com/mourisl/Rascaf"
-  doc_url: "https://github.com/mourisl/Rascaf/blob/v{{ version }}/README.md"
+  doc_url: "https://github.com/mourisl/Rascaf/blob/master/README.md"
 
 extra:
   additional-platforms:

From 7e7d7b79d1533d777ced957a0fcad03177ca537d Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Thu, 28 Aug 2025 17:37:51 +0800
Subject: [PATCH 15/15] update galaxy-ml

---
 recipes/galaxy-ml/meta.yaml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/recipes/galaxy-ml/meta.yaml b/recipes/galaxy-ml/meta.yaml
index 1151d1f393c6f..ce121904eec3e 100644
--- a/recipes/galaxy-ml/meta.yaml
+++ b/recipes/galaxy-ml/meta.yaml
@@ -9,22 +9,24 @@ source:
   sha256: 921a7884bfab3a7b40021e33602b13a9a5a2c58a3205c87659423ebd892476f1
 
 build:
-  number: 3
+  number: 4
+  run_exports:
+    - {{ pin_subpackage('galaxy-ml',max_pin="x.x") }}
   script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv
-  skip: True  # [osx or py<39 or py>39]
+  skip: True  # [osx]
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host:
-    - python
+    - python =3.9
     - cython
     - pip
     - setuptools
     - numpy >=1.22, <1.23
   run:
-    - python
+    - python =3.9
     - pyfaidx
     - pytabix
     - tabix
@@ -39,7 +41,7 @@ requirements:
     - mlxtend >=0.21, <0.22
     - skrebate >=0.60, <0.70
     - imbalanced-learn >=0.9, <0.10
-    - tensorflow >=2.10, <2.11
+    - tensorflow =2.10.0
     - keras >=2.10, <2.11
     - scikit-optimize >=0.9
     - plotly >=4.10.0, <5.0
@@ -79,3 +81,5 @@ about:
 extra:
   recipe-maintainers:
     - qiagu
+  additional-platforms:
+    - linux-aarch64