From 18a6a8eb38a35ea861351d8ced0d2b76d9a4a195 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 27 Aug 2024 10:55:51 -0500
Subject: [PATCH 01/14] spoa: add arm64 build (#50226)

* spoa: add arm64 build

* clean up recipe

* clean up recipe
---
 recipes/spoa/build.sh  | 16 ++++++++++++----
 recipes/spoa/meta.yaml | 13 +++++++++----
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/recipes/spoa/build.sh b/recipes/spoa/build.sh
index 925752eeaca8e..1f0c524a7b06f 100644
--- a/recipes/spoa/build.sh
+++ b/recipes/spoa/build.sh
@@ -4,7 +4,7 @@ set -eoux pipefail
 export INCLUDES="-I{PREFIX}/include"
 export LIBPATH="-L${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -O3"
+export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include"
 
 case $(uname -m) in
     x86_64)
@@ -13,21 +13,29 @@ case $(uname -m) in
     aarch64)
         SPOA_OPTS="-Dspoa_use_simde_nonvec=ON -DBUILD_TESTING=OFF"
         ;;
+    arm64)
+	SPOA_OPTS="-Dspoa_use_simde_nonvec=ON -DBUILD_TESTING=OFF"
+	;;
     *)
         ;;
 esac
 
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
 
 cmake -S . -B build \
 	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
 	-DCMAKE_BUILD_TYPE=Release \
-	-DBUILD_SHARED_LIBS=ON \
 	-Dspoa_install=ON \
 	-Dspoa_build_exe=ON \
-	${SPOA_OPTS} \
+	"${SPOA_OPTS}" \
 	-Dspoa_use_simde=ON \
 	-Dspoa_use_simde_openmp=ON \
+	-Dspoa_use_cereal=ON \
 	-DCMAKE_CXX_COMPILER="${CXX}" \
-	-DCMAKE_CXX_FLAGS="${CXXFLAGS}"
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" "${CONFIG_ARGS}"
 
 cmake --build build/ --target install -j ${CPU_COUNT} -v
diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml
index b4c53999344c7..ca3c358ba60bf 100644
--- a/recipes/spoa/meta.yaml
+++ b/recipes/spoa/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -23,9 +23,10 @@ requirements:
   host:
     - zlib
     - simde
-    - libgomp  # [linux]
+    - libgomp      # [linux]
     - llvm-openmp  # [osx]
-    - cpu_features
+    - cpu_features  # [linux]
+    - cereal
 
 test:
   commands:
@@ -34,12 +35,16 @@ test:
 about:
   home: 'https://github.com/rvaser/spoa'
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: 'SIMD partial order alignment tool/library'
+  summary: 'SIMD partial order alignment tool/library.'
+  dev_url: 'https://github.com/rvaser/spoa'
+  doc_url: 'https://github.com/rvaser/spoa/blob/{{ version }}/README.md'
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:spoa
     - doi:10.1101/gr.214270.116

From 3454fd8d9a8aa45864f1b0f214ac64feebce0b5f Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:03:16 -0400
Subject: [PATCH 02/14] Update gw to 1.0.3 (#50360)

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

diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml
index 4645b40c73b2c..ba0135f18a300 100644
--- a/recipes/gw/meta.yaml
+++ b/recipes/gw/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.2" %}
-{% set sha256 = "1f9b17702a073e255a87e5e273c0dd0ddafbc25c02b19aa143b3d744ce5d359d" %}
+{% set version = "1.0.3" %}
+{% set sha256 = "7247a8ec9efb7ebcd9566f6a3759520ee87f305efc91c8ce658307308ee6368a" %}
 
 package:
   name: gw

From bb39fc9fcbc0c48d9d2c3548337ce069cfb958fc Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:36:27 -0500
Subject: [PATCH 03/14] sorted_nearest: add arm64 build (#50361)

* sorted_nearest: add arm64 build

* edit license
---
 .../sorted_nearest/build_failure.osx-64.yaml  | 105 ------------------
 recipes/sorted_nearest/meta.yaml              |  18 ++-
 2 files changed, 12 insertions(+), 111 deletions(-)
 delete mode 100644 recipes/sorted_nearest/build_failure.osx-64.yaml

diff --git a/recipes/sorted_nearest/build_failure.osx-64.yaml b/recipes/sorted_nearest/build_failure.osx-64.yaml
deleted file mode 100644
index b28a52d273527..0000000000000
--- a/recipes/sorted_nearest/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: 2fa8de914f4d17ddde8039fbe1761352a875d48f192b025f668e9186e0a4edc9  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: test failure
-log: |2-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  WARNING: Importing conda-verify failed.  Please be sure to test your packages.  conda install conda-verify to make this message go away.
-  compiling .pyc files...
-  number of files: 54
-     INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']'
-     INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']'
-     INFO: sysroot: '/opt/X11/' files: '[]'
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/sorted_nearest.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/tiles.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/k_nearest.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/max_disjoint_intervals.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/clusters.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/k_nearest_ties.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/windows.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/introns.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/annotate_clusters.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/merge_by.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (sorted_nearest,lib/python3.9/site-packages/sorted_nearest/src/cluster_by.cpython-39-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-  WARNING (sorted_nearest): interpreter (Python) package conda-forge/osx-64::python==3.9.19=h7a9c478_0_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports)
-  Fixing permissions
-  INFO :: Time taken to mark (prefix)
-          0 replacements in 0 files was 0.06 seconds
-  TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2
-  Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work_moved_sorted_nearest-0.0.39-py39h1841df5_2_osx-64'
-  shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/work_moved_sorted_nearest-0.0.39-py39h1841df5_2_osx-64)
-  Reloading output folder (local): ...working... done
-  Solving environment (_test_env): ...working... done
-
-  ## Package Plan ##
-
-    environment location: /opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
-
-
-  The following NEW packages will be INSTALLED:
-
-      bzip2:           1.0.8-h10d778d_5          conda-forge
-      ca-certificates: 2024.6.2-h8857fd0_0       conda-forge
-      libblas:         3.9.0-22_osx64_openblas   conda-forge
-      libcblas:        3.9.0-22_osx64_openblas   conda-forge
-      libcxx:          17.0.6-h88467a6_0         conda-forge
-      libffi:          3.4.2-h0d85af4_5          conda-forge
-      libgfortran:     5.0.0-13_2_0_h97931a8_3   conda-forge
-      libgfortran5:    13.2.0-h2873a65_3         conda-forge
-      liblapack:       3.9.0-22_osx64_openblas   conda-forge
-      libopenblas:     0.3.27-openmp_hfef2a42_0  conda-forge
-      libsqlite:       3.46.0-h1b8f9f3_0         conda-forge
-      libzlib:         1.3.1-h87427d6_1          conda-forge
-      llvm-openmp:     18.1.7-h15ab845_0         conda-forge
-      ncurses:         6.5-h5846eda_0            conda-forge
-      numpy:           1.26.4-py39h28c39a1_0     conda-forge
-      openssl:         3.3.1-h87427d6_0          conda-forge
-      python:          3.9.19-h7a9c478_0_cpython conda-forge
-      python_abi:      3.9-4_cp39                conda-forge
-      readline:        8.2-h9e318b2_1            conda-forge
-      sorted_nearest:  0.0.39-py39h1841df5_2     local
-      tk:              8.6.13-h1abcd95_1         conda-forge
-      tzdata:          2024a-h0c530f3_0          conda-forge
-      xz:              5.2.6-h775f41a_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/test_tmp/run_test.py", line 2, in <module>
-      import sorted_nearest
-    File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.9/site-packages/sorted_nearest/__init__.py", line 1, in <module>
-      import pkg_resources
-  ModuleNotFoundError: No module named 'pkg_resources'
-  WARNING: Tests failed for sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
-  TESTS FAILED: sorted_nearest-0.0.39-py39h1841df5_2.tar.bz2
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1718121720195/test_tmp
-  import: 'sorted_nearest'
-# Last 100 lines of the build log.
diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml
index d6a32c10c8df0..6c2a719b9b627 100644
--- a/recipes/sorted_nearest/meta.yaml
+++ b/recipes/sorted_nearest/meta.yaml
@@ -4,7 +4,6 @@
 {% set hash_type = "sha256" %}
 {% set hash_value = "16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1" %}
 
-
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
@@ -14,8 +13,10 @@ source:
   '{{ hash_type }}': '{{ hash_value }}'
 
 build:
-  number: 2
-  script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
+  number: 3
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir"
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin='x.x') }}
 
@@ -24,8 +25,9 @@ requirements:
     - {{ compiler('c') }}
   host:
     - python
-    - setuptools
+    - pip
     - cython
+    - setuptools-scm >=6.2
   run:
     - python
     - numpy
@@ -36,9 +38,13 @@ test:
 
 about:
   home: https://github.com/endrebak/sorted_nearest
-  license: BSD
-  summary: Find nearest interval.
+  license: BSD-3-Clause
+  license_family: BSD
+  license_file: LICENSE.txt
+  summary: "Find nearest interval."
+  dev_url: https://github.com/endrebak/sorted_nearest
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64

From e675ac09c99a914a742992307e9cb7c8ff2560eb Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:36:38 -0500
Subject: [PATCH 04/14] Update flye to 2.9.5 (#50359)

---
 recipes/flye/build_failure.linux-64.yaml      | 104 ------------------
 recipes/flye/build_failure.linux-aarch64.yaml | 104 ------------------
 recipes/flye/build_failure.osx-64.yaml        | 104 ------------------
 recipes/flye/meta.yaml                        |   7 +-
 4 files changed, 3 insertions(+), 316 deletions(-)
 delete mode 100644 recipes/flye/build_failure.linux-64.yaml
 delete mode 100644 recipes/flye/build_failure.linux-aarch64.yaml
 delete mode 100644 recipes/flye/build_failure.osx-64.yaml

diff --git a/recipes/flye/build_failure.linux-64.yaml b/recipes/flye/build_failure.linux-64.yaml
deleted file mode 100644
index a406f2626fdcc..0000000000000
--- a/recipes/flye/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  Removed build tracker: '/tmp/pip-build-tracker-0s_3_n2n'
-
-  Resource usage statistics from building flye:
-     Process count: 20
-     CPU time: Sys=0:00:08.1, User=0:02:13.1
-     Memory: 1.6G
-     Disk usage: 252.4K
-     Time elapsed: 0:01:11.0
-
-
-  compiling .pyc files...
-  number of files: 104
-  Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-  Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-  Warning: rpath /opt/conda/conda-bld/flye_1717795145756/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717795145756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-     INFO: sysroot: '/opt/conda/conda-bld/flye_1717795145756/_build_env/x86_64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo/zone.tab', 'usr/share/zoneinfo/tzdata.zi', 'usr/share/zoneinfo/right/Zulu', 'usr/share/zoneinfo/right/WET']'
-     INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-minimap2): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6
-     INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-minimap2): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-modules): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6
-     INFO (flye,bin/flye-modules): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-64::libstdcxx-ng==13.2.0=hc0a3c3a_7
-     INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-modules): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-64::libgcc-ng==13.2.0=h77fa898_7
-     INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-modules): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-samtools): Needed DSO lib/libz.so.1 found in conda-forge/linux-64::libzlib==1.2.13=h4ab18f5_6
-     INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye,bin/flye-samtools): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.12=he073ed8_17
-     INFO (flye): Interpreted package 'flye' is interpreted by 'python'
-  Fixing permissions
-  Packaged license file/s.
-  INFO :: Time taken to mark (prefix)
-          0 replacements in 0 files was 0.07 seconds
-  Files containing CONDA_PREFIX
-  -----------------------------
-  bin/flye (text): Patching
-  TEST START: /opt/conda/conda-bld/linux-64/flye-2.9.4-py312ha1f7cf2_1.tar.bz2
-  Renaming work directory '/opt/conda/conda-bld/flye_1717795145756/work' to '/opt/conda/conda-bld/flye_1717795145756/work_moved_flye-2.9.4-py312ha1f7cf2_1_linux-64'
-  shutil.move(work)=/opt/conda/conda-bld/flye_1717795145756/work, dest=/opt/conda/conda-bld/flye_1717795145756/work_moved_flye-2.9.4-py312ha1f7cf2_1_linux-64)
-  Reloading output folder (local): ...working... done
-  Solving environment (_test_env): ...working... done
-
-  ## Package Plan ##
-
-    environment location: /opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
-
-
-  The following NEW packages will be INSTALLED:
-
-      _libgcc_mutex:    0.1-conda_forge           conda-forge
-      _openmp_mutex:    4.5-2_gnu                 conda-forge
-      bzip2:            1.0.8-hd590300_5          conda-forge
-      ca-certificates:  2024.6.2-hbcca054_0       conda-forge
-      flye:             2.9.4-py312ha1f7cf2_1     local
-      ld_impl_linux-64: 2.40-hf3520f5_2           conda-forge
-      libexpat:         2.6.2-h59595ed_0          conda-forge
-      libffi:           3.4.2-h7f98852_5          conda-forge
-      libgcc-ng:        13.2.0-h77fa898_7         conda-forge
-      libgomp:          13.2.0-h77fa898_7         conda-forge
-      libnsl:           2.0.1-hd590300_0          conda-forge
-      libsqlite:        3.45.3-h2797004_0         conda-forge
-      libstdcxx-ng:     13.2.0-hc0a3c3a_7         conda-forge
-      libuuid:          2.38.1-h0b41bf4_0         conda-forge
-      libxcrypt:        4.4.36-hd590300_1         conda-forge
-      libzlib:          1.3.1-h4ab18f5_1          conda-forge
-      ncurses:          6.5-h59595ed_0            conda-forge
-      openssl:          3.3.1-h4ab18f5_0          conda-forge
-      pip:              24.0-pyhd8ed1ab_0         conda-forge
-      python:           3.12.3-hab00c5b_0_cpython conda-forge
-      python_abi:       3.12-4_cp312              conda-forge
-      readline:         8.2-h8228510_1            conda-forge
-      setuptools:       70.0.0-pyhd8ed1ab_0       conda-forge
-      tk:               8.6.13-noxft_h4845f30_101 conda-forge
-      tzdata:           2024a-h0c530f3_0          conda-forge
-      wheel:            0.43.0-pyhd8ed1ab_1       conda-forge
-      xz:               5.2.6-h166bdaf_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-  export PREFIX=/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
-  export SRC_DIR=/opt/conda/conda-bld/flye_1717795145756/test_tmp
-   flye -h
-   grep Assembly
-  Traceback (most recent call last):
-    File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/flye", line 7, in <module>
-      from flye.main import main
-    File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/main.py", line 19, in <module>
-      import flye.polishing.alignment as aln
-    File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/polishing/alignment.py", line 18, in <module>
-      import flye.utils.fasta_parser as fp
-    File "/opt/conda/conda-bld/flye_1717795145756/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/utils/fasta_parser.py", line 26, in <module>
-      from flye.six.moves import range
-  ModuleNotFoundError: No module named 'flye.six.moves'
-  WARNING: Tests failed for flye-2.9.4-py312ha1f7cf2_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
-  TESTS FAILED: flye-2.9.4-py312ha1f7cf2_1.tar.bz2
-# Last 100 lines of the build log.
diff --git a/recipes/flye/build_failure.linux-aarch64.yaml b/recipes/flye/build_failure.linux-aarch64.yaml
deleted file mode 100644
index d451186baca31..0000000000000
--- a/recipes/flye/build_failure.linux-aarch64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-     CPU time: Sys=0:00:04.6, User=0:01:53.3
-     Memory: 1.7G
-     Disk usage: 289.9K
-     Time elapsed: 0:01:33.1
-
-
-  Packaging flye
-  Packaging flye-2.9.4-py312h747c3d4_1
-  compiling .pyc files...
-  number of files: 104
-  Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-  Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-  Warning: rpath /opt/conda/conda-bld/flye_1717793573507/_build_env/lib is outside prefix /opt/conda/conda-bld/flye_1717793573507/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
-     INFO: sysroot: '/opt/conda/conda-bld/flye_1717793573507/_build_env/aarch64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo/zone1970.tab', 'usr/share/zoneinfo/zone.tab', 'usr/share/zoneinfo/tzdata.zi', 'usr/share/zoneinfo/right/Zulu']'
-     INFO (flye,bin/flye-modules): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6
-     INFO (flye,bin/flye-modules): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-aarch64::libstdcxx-ng==13.2.0=h3f4de04_7
-     INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-modules): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-aarch64::libgcc-ng==13.2.0=he277a41_7
-     INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-modules): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-minimap2): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6
-     INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-minimap2): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-samtools): Needed DSO lib/libz.so.1 found in conda-forge/linux-aarch64::libzlib==1.2.13=h68df207_6
-     INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libdl.so.2 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye,bin/flye-samtools): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_14
-     INFO (flye): Interpreted package 'flye' is interpreted by 'python'
-  Fixing permissions
-  Packaged license file/s.
-  INFO :: Time taken to mark (prefix)
-          0 replacements in 0 files was 0.13 seconds
-  Files containing CONDA_PREFIX
-  -----------------------------
-  bin/flye (text): Patching
-  WARNING: Importing conda-verify failed.  Please be sure to test your packages.  conda install conda-verify to make this message go away.
-  TEST START: /opt/conda/conda-bld/linux-aarch64/flye-2.9.4-py312h747c3d4_1.tar.bz2
-  Renaming work directory '/opt/conda/conda-bld/flye_1717793573507/work' to '/opt/conda/conda-bld/flye_1717793573507/work_moved_flye-2.9.4-py312h747c3d4_1_linux-aarch64'
-  shutil.move(work)=/opt/conda/conda-bld/flye_1717793573507/work, dest=/opt/conda/conda-bld/flye_1717793573507/work_moved_flye-2.9.4-py312h747c3d4_1_linux-aarch64)
-  Reloading output folder (local): ...working... done
-  Solving environment (_test_env): ...working... done
-
-  ## Package Plan ##
-
-    environment location: /opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
-
-
-  The following NEW packages will be INSTALLED:
-
-      _openmp_mutex:         4.5-2_gnu                 conda-forge
-      bzip2:                 1.0.8-h31becfc_5          conda-forge
-      ca-certificates:       2024.6.2-hcefe29a_0       conda-forge
-      flye:                  2.9.4-py312h747c3d4_1     local
-      ld_impl_linux-aarch64: 2.40-h9fc2d93_2           conda-forge
-      libexpat:              2.6.2-h2f0025b_0          conda-forge
-      libffi:                3.4.2-h3557bc0_5          conda-forge
-      libgcc-ng:             13.2.0-he277a41_7         conda-forge
-      libgomp:               13.2.0-he277a41_7         conda-forge
-      libnsl:                2.0.1-h31becfc_0          conda-forge
-      libsqlite:             3.45.3-h194ca79_0         conda-forge
-      libstdcxx-ng:          13.2.0-h3f4de04_7         conda-forge
-      libuuid:               2.38.1-hb4cce97_0         conda-forge
-      libxcrypt:             4.4.36-h31becfc_1         conda-forge
-      libzlib:               1.3.1-h68df207_1          conda-forge
-      ncurses:               6.5-h0425590_0            conda-forge
-      openssl:               3.3.1-h68df207_0          conda-forge
-      pip:                   24.0-pyhd8ed1ab_0         conda-forge
-      python:                3.12.3-h43d1f9e_0_cpython conda-forge
-      python_abi:            3.12-4_cp312              conda-forge
-      readline:              8.2-h8fc344f_1            conda-forge
-      setuptools:            70.0.0-pyhd8ed1ab_0       conda-forge
-      tk:                    8.6.13-h194ca79_0         conda-forge
-      tzdata:                2024a-h0c530f3_0          conda-forge
-      wheel:                 0.43.0-pyhd8ed1ab_1       conda-forge
-      xz:                    5.2.6-h9cdd2b7_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-  export PREFIX=/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
-  export SRC_DIR=/opt/conda/conda-bld/flye_1717793573507/test_tmp
-   flye -h
-   grep Assembly
-  Traceback (most recent call last):
-    File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/flye", line 7, in <module>
-      from flye.main import main
-    File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/main.py", line 19, in <module>
-      import flye.polishing.alignment as aln
-    File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/polishing/alignment.py", line 18, in <module>
-      import flye.utils.fasta_parser as fp
-    File "/opt/conda/conda-bld/flye_1717793573507/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/flye/utils/fasta_parser.py", line 26, in <module>
-      from flye.six.moves import range
-  ModuleNotFoundError: No module named 'flye.six.moves'
-  WARNING: Tests failed for flye-2.9.4-py312h747c3d4_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
-  TESTS FAILED: flye-2.9.4-py312h747c3d4_1.tar.bz2
-# Last 100 lines of the build log.
diff --git a/recipes/flye/build_failure.osx-64.yaml b/recipes/flye/build_failure.osx-64.yaml
deleted file mode 100644
index 453ba051fb8e3..0000000000000
--- a/recipes/flye/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 577df4f0a9db63e97ed56cec147ab74fc83826ef97945bc3489ec47ece2f4725  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-      make:                4.3-h22f3db7_1            conda-forge
-      openssl:             3.3.1-h87427d6_0          conda-forge
-      sigtool:             0.1.3-h88f4db0_0          conda-forge
-      tapi:                1100.0.11-h9ce4665_0      conda-forge
-      xz:                  5.2.6-h775f41a_0          conda-forge
-      zstd:                1.5.6-h915ae27_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-  Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache
-  Downloading source to cache: 2.9.4_197a2dfe39.tar.gz
-  Downloading https://github.com/fenderglass/Flye/archive/2.9.4.tar.gz
-  Success
-  checking file Makefile
-  patching file Makefile
-  /opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/python: No module named pip
-  Extracting download
-  Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/flye/0001-Makefile-aarch64.patch
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-  Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/flye/0001-Makefile-aarch64.patch with args:
-  ['-Np1', '-i', '/tmp/tmpfu1zkvqb/0001-Makefile-aarch64.patch.native', '--binary']
-  Patch analysis gives:
-      utils.check_call_env(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-  [[ RA-MD1LOVE ]] - [[                                             0001-Makefile-aarch64.patch ]]
-
-  Key:
-
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  R :: Reversible                       A :: Applicable
-  Y :: Build-prefix patch in use        M :: Minimal, non-amalgamated
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work/conda_build.sh']' returned non-zero exit status 1.
-  D :: Dry-runnable                     N :: Patch level (1 is preferred)
-  L :: Patch level not-ambiguous        O :: Patch applies without offsets
-  V :: Patch applies without fuzz       E :: Patch applies without emitting to stderr
-
-  source tree in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold
-  export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/_build_env
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/flye_1717794246060/work
-  INFO: activate_clang_osx-64.sh made the following environmental changes:
-  AR=x86_64-apple-darwin13.4.0-ar
-  AS=x86_64-apple-darwin13.4.0-as
-  CC=x86_64-apple-darwin13.4.0-clang
-  CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
-  CLANG=x86_64-apple-darwin13.4.0-clang
-  CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
-  CMAKE_PREFIX_PATH=:$PREFIX
-  CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
-  CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
-  CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
-  DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  HOST=x86_64-apple-darwin13.4.0
-  INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
-  LD=x86_64-apple-darwin13.4.0-ld
-  LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
-  LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
-  LIBTOOL=x86_64-apple-darwin13.4.0-libtool
-  LIPO=x86_64-apple-darwin13.4.0-lipo
-  MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
-  NM=x86_64-apple-darwin13.4.0-nm
-  NMEDIT=x86_64-apple-darwin13.4.0-nmedit
-  OBJC=x86_64-apple-darwin13.4.0-clang
-  OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  OTOOL=x86_64-apple-darwin13.4.0-otool
-  PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
-  RANLIB=x86_64-apple-darwin13.4.0-ranlib
-  REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
-  SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
-  SEGEDIT=x86_64-apple-darwin13.4.0-segedit
-  SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
-  SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-  INFO: activate_clangxx_osx-64.sh made the following environmental changes:
-  CLANGXX=x86_64-apple-darwin13.4.0-clang
-  CXX=x86_64-apple-darwin13.4.0-clang
-  CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/flye-2.9.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-# Last 100 lines of the build log.
diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml
index 4cc8f7c9eb91a..c3e7e7cef65fb 100644
--- a/recipes/flye/meta.yaml
+++ b/recipes/flye/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "flye" %}
-{% set version = "2.9.4" %}
-{% set sha256 = "197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696" %}
+{% set version = "2.9.5" %}
+{% set sha256 = "7b384266d83b1e66bcaf82d49d35ac6c587bad9146e8f3b752a220291f6b1a6f" %}
 
 package:
   name: {{ name }}
@@ -13,8 +13,7 @@ source:
     - 0001-Makefile-aarch64.patch
 
 build:
-  number: 2
-  skip: True  # [py > 311]
+  number: 0
   entry_points:
     - flye = flye.main:main
   run_exports:

From 2ab11d76aeb187d010be885ba94c33243fc8171e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:58:30 -0400
Subject: [PATCH 05/14] Update nextstrain-cli to 8.5.2 (#50363)

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

diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml
index 6d6f19923748b..7d4034a370549 100644
--- a/recipes/nextstrain-cli/meta.yaml
+++ b/recipes/nextstrain-cli/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "8.5.1" %}
+{% set version = "8.5.2" %}
 
 package:
   name: nextstrain-cli
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz
-  sha256: 5318296512acc4e47fe7d0ffa11b0654ec47ad7822006be3b75864f17b94ea67
+  sha256: 1c7a1a0fac911c8b6e70b6be296e48e7abb3ff38262abc2f62d185f567ac24d6
 
 build:
   number: 0

From bec54887620139c54741c9dca280d17977706bd5 Mon Sep 17 00:00:00 2001
From: kdc10 <66701561+kdc10@users.noreply.github.com>
Date: Tue, 27 Aug 2024 21:59:11 +0200
Subject: [PATCH 06/14] Update emu v3.4.6 (#50353)

* Update emu v3.4.6

* change url to github

* add run_scports
---
 recipes/emu/meta.yaml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/recipes/emu/meta.yaml b/recipes/emu/meta.yaml
index ad6bd76d68361..afaf213e3773d 100644
--- a/recipes/emu/meta.yaml
+++ b/recipes/emu/meta.yaml
@@ -1,18 +1,21 @@
 {% set name = "emu" %}
-{% set version = "3.4.5" %}
+{% set version = "3.4.6" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: 'https://gitlab.com/treangenlab/emu/-/archive/v{{version}}/emu-v{{version}}.tar.gz'
-  sha256: a77a3d362384d8e12bbb5f75dc74eaf0f04faec1e4f69195b9e92bc7c025296e
+  url: 'https://github.com/treangenlab/emu/archive/refs/tags/v{{version}}.tar.gz'
+  sha256: 9c7dab900ad6c3e8689733778a0ecfd8ebb15733e3c45f6ec3a7c32b8cb06805
 
 build:
   noarch: generic
   number: 0
   script: mkdir -p ${PREFIX}/bin && cp emu ${PREFIX}/bin
+  
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   run:
@@ -36,7 +39,7 @@ test:
     - emu --help 
 
 about:
-  home: https://gitlab.com/treangenlab/emu
+  home: https://github.com/treangenlab/emu
   license: MIT
   license_file: LICENSE.txt
   summary: Emu is a relative abundance estimator for 16s genomic data.

From 098846a80bb227d2faa4527449fffc0c35ad5bef Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 27 Aug 2024 22:10:27 -0400
Subject: [PATCH 07/14] Update methbat to 0.13.2 (#50365)

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

diff --git a/recipes/methbat/meta.yaml b/recipes/methbat/meta.yaml
index 33388fb2c43a5..3a568f5b18909 100644
--- a/recipes/methbat/meta.yaml
+++ b/recipes/methbat/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "methbat" %}
-{% set version = "0.13.1" %}
-{% set sha256 = "79e3e48edda49d31601a58252a5e4b5a0d2d35900208df97f16de66712d6ba56" %}
+{% set version = "0.13.2" %}
+{% set sha256 = "3a3a6374170e8b2acdc5e2c160eaabdafe5d613139d0c798438794ea35bff6c5" %}
 
 package:
   name: {{ name }}

From 81ab4f7258ef01a85ed56d465027e874af817996 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 27 Aug 2024 22:10:42 -0400
Subject: [PATCH 08/14] Update pbstarphase to 0.14.1 (#50364)

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

diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml
index 829520935dfff..20e9abaa3900a 100644
--- a/recipes/pbstarphase/meta.yaml
+++ b/recipes/pbstarphase/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbstarphase" %}
-{% set version = "0.14.0" %}
-{% set sha256 = "5397c43338d006d65aa36c07d6299bf8c60c071138f0325760d32e65957d236d" %}
+{% set version = "0.14.1" %}
+{% set sha256 = "d49a9a20c40edac7e35cbd9d87beabb78166ea08af8538eb3d3492a03d2d5425" %}
 
 package:
   name: {{ name }}

From e432de98e9438e2c120a1a3b58c1ce9d9a6c1976 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 27 Aug 2024 22:30:16 -0500
Subject: [PATCH 09/14] Update meme to 5.5.7 (#50367)

---
 recipes/meme/build.sh  | 13 +++----------
 recipes/meme/meta.yaml |  9 +++------
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/recipes/meme/build.sh b/recipes/meme/build.sh
index 7873b96820409..30440594b5d6a 100644
--- a/recipes/meme/build.sh
+++ b/recipes/meme/build.sh
@@ -1,10 +1,10 @@
 #!/bin/bash -ex
 
 export MEME_ETC_DIR="${PREFIX}/etc"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
 
-autoreconf -i
-
-perl scripts/dependencies.pl
+autoreconf -if
 
 ./configure CC="${CC}" \
 	CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include" \
@@ -14,13 +14,6 @@ perl scripts/dependencies.pl
 	--enable-build-libxslt
 
 make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j"${CPU_COUNT}"
-
-# tests will only work inside the build dir, but
-# https://github.com/conda/conda-build/issues/1453
-# so you need `conda build --prefix-length 1`
-# for it to work properly
-# make test
-
 make install
 make clean
 
diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml
index 5e8ace3b3461a..b44bef89008de 100644
--- a/recipes/meme/meta.yaml
+++ b/recipes/meme/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "MEME" %}
-{% set version = "5.5.6" %}
-{% set sha256 = "8f719002c3a2177f6bb9da6861098ccf4f08b3006f002a88bb3afe9473596c67" %}
+{% set version = "5.5.7" %}
+{% set sha256 = "1dca8d0e6d1d36570c1a88ab8dbe7e4b177733fbbeacaa2e8c4674febf57aaf4" %}
 
 package:
   name: {{ name|lower }}
@@ -12,7 +12,6 @@ source:
 
 build:
   number: 0
-  detect_binary_files_with_prefix: True
   run_exports:
     - {{ pin_subpackage("meme", max_pin="x") }}
 
@@ -27,11 +26,9 @@ requirements:
     - nodejs >=16.4.1
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
-    - yaml
-    - icu >=72.1,<73.0a0
+    - icu
     - ghostscript
     - zlib
-    - xz
     - libxslt
     - libxml2
     - expat

From 770b5e61f58969f2f6304f1e3a2bf5758252c8d8 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Wed, 28 Aug 2024 01:53:04 -0500
Subject: [PATCH 10/14] ucsc-bigwigsummary: update macOS build (#50368)

* ucsc-bigwigsummary: update macOS build

* edit build.sh

* edit meta.yaml
---
 recipes/ucsc-bigwigsummary/build.sh           | 29 ++++++++++++++-----
 recipes/ucsc-bigwigsummary/htmshell.patch     | 11 -------
 .../ucsc-bigwigsummary/include.macos.patch    | 27 +++++++++++++++++
 recipes/ucsc-bigwigsummary/meta.yaml          | 27 +++++++++--------
 4 files changed, 63 insertions(+), 31 deletions(-)
 delete mode 100644 recipes/ucsc-bigwigsummary/htmshell.patch
 create mode 100644 recipes/ucsc-bigwigsummary/include.macos.patch

diff --git a/recipes/ucsc-bigwigsummary/build.sh b/recipes/ucsc-bigwigsummary/build.sh
index bc10870454d00..603cc567834b8 100644
--- a/recipes/ucsc-bigwigsummary/build.sh
+++ b/recipes/ucsc-bigwigsummary/build.sh
@@ -1,13 +1,26 @@
 #!/bin/bash
+
 mkdir -p "$PREFIX/bin"
+
 export MACHTYPE=$(uname -m)
-export BINDIR=$(pwd)/bin
+export BINDIR="$(pwd)/bin"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
 export L="${LDFLAGS}"
+
 mkdir -p "$BINDIR"
-(cd kent/src/lib && make -j ${CPU_COUNT})
-(cd kent/src/htslib && make -j ${CPU_COUNT})
-(cd kent/src/jkOwnLib && make -j ${CPU_COUNT})
-(cd kent/src/hg/lib && make -j ${CPU_COUNT})
-(cd kent/src/utils/bigWigSummary && make -j ${CPU_COUNT})
-cp bin/bigWigSummary "$PREFIX/bin"
-chmod +x "$PREFIX/bin/bigWigSummary"
+
+if [[ "$(uname)" == Darwin ]]; then
+	export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+	export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument"
+fi
+
+(cd kent/src/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/htslib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/jkOwnLib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/hg/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/utils/bigWigSummary && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+cp -rf bin/bigWigSummary "$PREFIX/bin"
+chmod 0755 "$PREFIX/bin/bigWigSummary"
diff --git a/recipes/ucsc-bigwigsummary/htmshell.patch b/recipes/ucsc-bigwigsummary/htmshell.patch
deleted file mode 100644
index 1e6f87375ed01..0000000000000
--- a/recipes/ucsc-bigwigsummary/htmshell.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- kent/src/lib/htmshell.c	2024-03-27 10:56:44.493892141 +0200
-+++ kent/src/lib/htmshell.c	2024-03-27 10:57:01.073792396 +0200
-@@ -713,7 +713,7 @@
- puts("Status: 400\r");
- puts("Content-Type: text/plain; charset=UTF-8\r");
- puts("\r");
--if (format != NULL && args != NULL)
-+if (format != NULL)
-     {
-     vfprintf(stdout, format, args);
-     fprintf(stdout, "\n");
diff --git a/recipes/ucsc-bigwigsummary/include.macos.patch b/recipes/ucsc-bigwigsummary/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-bigwigsummary/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml
index ca2ca18d6646b..76a38a7d908f4 100644
--- a/recipes/ucsc-bigwigsummary/meta.yaml
+++ b/recipes/ucsc-bigwigsummary/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-bigwigsummary" %}
 {% set program = "bigWigSummary" %}
-{% set version = "448" %}
-{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %}
+{% set version = "469" %}
+{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
 
 package:
   name: {{ package }}
@@ -11,12 +11,11 @@ source:
   url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz
   sha256: {{ sha256 }}
   patches:
-    - include.patch
-    - htmshell.patch
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
   number: 1
-  skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(package|lower, max_pin=None) }}
 
@@ -25,29 +24,33 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - binutils # [linux]
+    - binutils  # [linux]
   host:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - mariadb-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
   run:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - mariadb-connector-c
+    - libopenssl-static
 
 test:
   commands:
-    # just check for existence, because the individual packages have no unified behavior
-    - which {{ program }}
+    # just check for existence and exec bit, because the individual packages have no unified behavior
+    - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "varies; see http://genome.ucsc.edu/license"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see http://genome.ucsc.edu/license"
   summary: "Extract summary information from a bigWig file."
+  dev_url: "https://github.com/ucscGenomeBrowser/kent"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   additional-platforms:

From fbc27ac5c441c7dc7e4d4c8293a31058871c1393 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Wed, 28 Aug 2024 03:44:32 -0500
Subject: [PATCH 11/14] ucsc-fatotwobit: update macOS build (#50369)

* ucsc-fatotwobit: update macOS build

* try without mariadb
---
 recipes/ucsc-fatotwobit/build.sh            | 29 +++++++++++++-----
 recipes/ucsc-fatotwobit/htmshell.patch      | 11 -------
 recipes/ucsc-fatotwobit/include.macos.patch | 27 ++++++++++++++++
 recipes/ucsc-fatotwobit/include.patch       | 16 +++++-----
 recipes/ucsc-fatotwobit/meta.yaml           | 34 ++++++++++-----------
 5 files changed, 72 insertions(+), 45 deletions(-)
 delete mode 100644 recipes/ucsc-fatotwobit/htmshell.patch
 create mode 100644 recipes/ucsc-fatotwobit/include.macos.patch

diff --git a/recipes/ucsc-fatotwobit/build.sh b/recipes/ucsc-fatotwobit/build.sh
index cd1c569ec1e88..017f496c75e0d 100644
--- a/recipes/ucsc-fatotwobit/build.sh
+++ b/recipes/ucsc-fatotwobit/build.sh
@@ -1,13 +1,26 @@
 #!/bin/bash
+
 mkdir -p "$PREFIX/bin"
+
 export MACHTYPE=$(uname -m)
-export BINDIR=$(pwd)/bin
+export BINDIR="$(pwd)/bin"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
 export L="${LDFLAGS}"
+
 mkdir -p "$BINDIR"
-(cd kent/src/lib && make)
-(cd kent/src/htslib && make)
-(cd kent/src/jkOwnLib && make)
-(cd kent/src/hg/lib && make)
-(cd kent/src/utils/faToTwoBit && make)
-cp bin/faToTwoBit "$PREFIX/bin"
-chmod +x "$PREFIX/bin/faToTwoBit"
+
+if [[ "$(uname)" == Darwin ]]; then
+        export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+        export CFLAGS="${CFLAGS} -Wno-unused-command-line-argument"
+fi
+
+(cd kent/src/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/htslib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/jkOwnLib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/hg/lib && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+(cd kent/src/utils/faToTwoBit && make CC="${CC}" CFLAGS="${CFLAGS}" -j ${CPU_COUNT})
+cp -rf bin/faToTwoBit "$PREFIX/bin"
+chmod 0755 "$PREFIX/bin/faToTwoBit"
diff --git a/recipes/ucsc-fatotwobit/htmshell.patch b/recipes/ucsc-fatotwobit/htmshell.patch
deleted file mode 100644
index 1e6f87375ed01..0000000000000
--- a/recipes/ucsc-fatotwobit/htmshell.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- kent/src/lib/htmshell.c	2024-03-27 10:56:44.493892141 +0200
-+++ kent/src/lib/htmshell.c	2024-03-27 10:57:01.073792396 +0200
-@@ -713,7 +713,7 @@
- puts("Status: 400\r");
- puts("Content-Type: text/plain; charset=UTF-8\r");
- puts("\r");
--if (format != NULL && args != NULL)
-+if (format != NULL)
-     {
-     vfprintf(stdout, format, args);
-     fprintf(stdout, "\n");
diff --git a/recipes/ucsc-fatotwobit/include.macos.patch b/recipes/ucsc-fatotwobit/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-fatotwobit/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-fatotwobit/include.patch b/recipes/ucsc-fatotwobit/include.patch
index e9c8621194325..2c1e8a7f20226 100644
--- a/recipes/ucsc-fatotwobit/include.patch
+++ b/recipes/ucsc-fatotwobit/include.patch
@@ -1,5 +1,5 @@
---- kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
-+++ kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
 @@ -17,7 +17,7 @@
  endif
  
@@ -9,24 +9,24 @@
  
  # to check for Mac OSX Darwin specifics:
  UNAME_S := $(shell uname -s)
---- kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
-+++ kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
+--- a/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
++++ b/kent/src/inc/common.mk	2022-10-25 12:00:00.000000000 +0100
 @@ -147,4 +147,4 @@
 -       L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl
 +       L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl
     else
       ifneq ($(wildcard /opt/local/lib/libssl.a),)
           L+=/opt/local/lib/libssl.a
---- kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
-+++ kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
 @@ -1,4 +1,4 @@
 -KENT_INC=-I../../../inc
 +KENT_INC=-I../../../inc -I${PREFIX}/include
 
  straw: straw.o cStraw.o
  	ld -r -o ../straw.o straw.o cStraw.o
---- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
-+++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python2.7
 +#!/usr/bin/env python
diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml
index 4a21a851c4e54..492d7f4a37cdd 100644
--- a/recipes/ucsc-fatotwobit/meta.yaml
+++ b/recipes/ucsc-fatotwobit/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-fatotwobit" %}
 {% set program = "faToTwoBit" %}
-{% set version = "455" %}
-{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %}
+{% set version = "469" %}
+{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
 
 package:
   name: "{{ package }}"
@@ -11,15 +11,11 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
-    - htmshell.patch
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True # [osx]
-  number: 2
-  ignore_run_exports:
-    - libpng
-    - libuuid
+  number: 1
   run_exports:
     - {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }}
 
@@ -28,29 +24,31 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - binutils # [linux]
+    - binutils  # [linux]
   host:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
     - libopenssl-static
-    - zlib >=1.3.1,<2.0a0
+    - clangdev  # [osx]
+    - zlib
   run:
     - libpng
     - libuuid
     - mysql-connector-c
-    - openssl
+    - libopenssl-static
 
 test:
   commands:
-    # just check for existence, because the individual packages have no unified behavior
-    - which {{ program }}
+    # just check for existence and exec bit, because the individual packages have no unified behavior
+    - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "varies; see http://genome.ucsc.edu/license"
-  summary: "Convert DNA from fasta to 2bit format"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see http://genome.ucsc.edu/license"
+  summary: "Convert DNA from fasta to 2bit format."
+  dev_url: "https://github.com/ucscGenomeBrowser/kent"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   additional-platforms:

From 225e66338a1ec62f40dcb2bd046d6321552eae69 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 28 Aug 2024 12:29:49 +0200
Subject: [PATCH 12/14] bump WisecondorX to v1.2.8 (#50374)

---
 recipes/wisecondorx/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/wisecondorx/meta.yaml b/recipes/wisecondorx/meta.yaml
index c32c17e5562fa..cd381550d1544 100644
--- a/recipes/wisecondorx/meta.yaml
+++ b/recipes/wisecondorx/meta.yaml
@@ -1,11 +1,11 @@
-{% set version="1.2.7" %}
+{% set version="1.2.8" %}
 package:
   name: wisecondorx
   version:  {{ version }}
 
 source:
   url: https://github.com/CenterForMedicalGeneticsGhent/wisecondorX/archive/v{{ version }}.tar.gz
-  sha256: 4597377e664afd5b4d78f92061d854186bbaba92ba9951f034e9e7ce4c2d1c29
+  sha256: 9460649cdfd36fd4edb74c89618a4fbecefa857f9bfa357d76898f7de433b131
 
 build:
   number: 0
@@ -19,6 +19,7 @@ requirements:
     - python >=3.6
     - setuptools
   run:
+    - pandas
     - python >=3.6
     - pysam
     - scipy

From 3b9a0262d7533fd4ca5bf9f27b0811692312fb4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Patrick=20K=C3=B6nig?=
 <35546377+patrick-koenig@users.noreply.github.com>
Date: Wed, 28 Aug 2024 13:31:39 +0200
Subject: [PATCH 13/14] Add blast2galaxy (#50375)

* Added meta.yaml for blast2galaxy

* Updated recipe for blast2galaxy
---
 recipes/blast2galaxy/meta.yaml | 52 ++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 recipes/blast2galaxy/meta.yaml

diff --git a/recipes/blast2galaxy/meta.yaml b/recipes/blast2galaxy/meta.yaml
new file mode 100644
index 0000000000000..91ee70dd020be
--- /dev/null
+++ b/recipes/blast2galaxy/meta.yaml
@@ -0,0 +1,52 @@
+{% set name = "blast2galaxy" %}
+{% set version = "0.1.0a1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/blast2galaxy-{{ version }}.tar.gz
+  sha256: ec1934a5a0e23a06175814790e6e9cefcbccadf52a7752f8278788b48b45eb4e
+
+build:
+  entry_points:
+    - blast2galaxy = blast2galaxy.cli:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('blast2galaxy', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10,<4.0
+    - poetry-core >=1.0.0
+    - pip
+  run:
+    - python >=3.10,<4.0
+    - typer >=0.9.0,<0.10.0
+    - bioblend >=1.2.0,<2.0.0
+    - rich >=13.6.0,<14.0.0
+    - tomli >=2.0.1,<3.0.0
+
+test:
+  imports:
+    - blast2galaxy
+  commands:
+    - pip check
+    - blast2galaxy --help
+  requires:
+    - pip
+
+about:
+  summary: A Python package with a CLI and API to perform BLAST queries against Galaxy servers
+  license: MIT
+  license_file: LICENSE
+  home: "https://github.com/IPK-BIT/blast2galaxy"
+  doc_url: "https://ipk-bit.github.io/blast2galaxy/"
+  dev_url: "https://github.com/IPK-BIT/blast2galaxy"
+
+extra:
+  recipe-maintainers:
+    - patrick-koenig

From fd4d29d55fae468bcfc50307adcdc620f42687fb Mon Sep 17 00:00:00 2001
From: Anuradha <anuradhawick@gmail.com>
Date: Wed, 28 Aug 2024 21:01:48 +0930
Subject: [PATCH 14/14] Update kmertools to v0.1.3 (#50370)

---
 recipes/kmertools/build.sh  | 2 +-
 recipes/kmertools/meta.yaml | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/kmertools/build.sh b/recipes/kmertools/build.sh
index 1f86b1f9190de..472a714ec66c5 100644
--- a/recipes/kmertools/build.sh
+++ b/recipes/kmertools/build.sh
@@ -31,7 +31,7 @@ fi
 # Build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build with maturin
-maturin build -m ./pykmertools/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip
+maturin build -m ./conda/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip
 
 # Install the wheel file
 ${PYTHON} -m pip install ./target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/kmertools/meta.yaml b/recipes/kmertools/meta.yaml
index 18f8c00e7dcd2..2ead57a35b7be 100644
--- a/recipes/kmertools/meta.yaml
+++ b/recipes/kmertools/meta.yaml
@@ -1,13 +1,13 @@
-{% set version = "0.1.2" %}
+{% set version = "0.1.3" %}
 {% set name = "kmertools" %}
-{% set sha256 = "0dfade580e1fbf6ba2bc1665792ae74b918bbe0cd5272c5f52bf553eee285a71" %}
+{% set sha256 = "02892ce148db4043bede10267f390c9fea14d49f65b43e1f05092153939bd5e0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 39]
   run_exports:
     - {{ pin_subpackage('kmertools', max_pin="x.x") }}