Merge branch 'master' into bump/starfish

recipes/afpdb/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
+  sha256: aad8f90092630dce86254227bc94e4f42a28598a6ccf69f07d0e619bc88c0ae8
 
 build:
   number: 0

recipes/devider/build.sh

@@ -1,10 +1,21 @@
-#!/bin/bash -euo
+#!/bin/bash
+
+set -xeuo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
 # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+export CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
 cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
-RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+
+case $(uname -m) in
+    aarch64 | arm64)
+        FEATURES="--features neon --no-default-features"
+        ;;
+    *)
+        FEATURES=""
+        ;;
+esac
+
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . ${FEATURES}
 cp scripts/* $PREFIX/bin

recipes/devider/devider-aarch64.patch

@@ -0,0 +1,14 @@
+--- Cargo.toml.orig	2024-10-14 10:59:48.140000000 +0000
++++ Cargo.toml	2024-10-14 11:03:33.120000000 +0000
+@@ -13,9 +13,9 @@
+ rayon="1.7"
+ rand="0.8"
+ rand_core="0.6"
+-rust-htslib= { version = "0.44", default-features = false }
++rust-htslib= { version = "0.47", default-features = false }
+ clap = { version = "=4.2.0", features = ["derive"] }
+-block-aligner = { version = "0.4", default-features = false }
++block-aligner = { version = "0.5", default-features = false }
+ debruijn = "0.3"
+ simple_logger="4"
+ log="0.4"

recipes/devider/meta.yaml

@@ -7,9 +7,11 @@ package:
 source:
   url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
   sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+  patches:
+    - devider-aarch64.patch # [aarch64]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('devider', max_pin="x.x") }}
 
@@ -20,6 +22,8 @@ requirements:
     - cargo-bundle-licenses
     - make
     - cmake >=3.12
+  host:
+    - clangdev >=16,<17 # [linux and aarch64]
   run:
     - python 
     - samtools
@@ -43,5 +47,7 @@ about:
   summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - bluenote-1577

recipes/easypqp/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "easypqp" %}
-{% set version = "0.1.49" %}
-{% set sha256 = "96fffd59e617de0007f1fbe88ab223d605a7d4a4e94a7b4f4d4a94b4016e327c" %}
+{% set version = "0.1.50" %}
+{% set sha256 = "d3ebc1c7cbe61f081c5ab71e76e7130aa7fae955895ffe8f719363b29870a000" %}
 
 package:
   name: {{ name|lower }}
@@ -23,6 +23,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - numba

recipes/fmsi/0001-Makefile.patch

@@ -0,0 +1,29 @@
+diff --git a/src/Makefile b/src/Makefile
+index 6272ad5..473407a 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,10 +1,10 @@
+ .PHONY: all clean 
+-CXX=									g++
+-CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O2
+-PROG=									../fmsi
+-INCLUDES-PATH?=.
++CXX=									${CXX}
++CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O3
++PROG=									${PREFIX}/bin/fmsi
++INCLUDES-PATH?=							${PREFIX}
+ INCLUDES=							-I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib 
+-LIBS=									-lz -lsdsl -ldivsufsort -ldivsufsort64
++LIBS+=									-lz -lsdsl -ldivsufsort -ldivsufsort64 -L${PREFIX}/lib
+
+ all:$(PROG)
+
+@@ -14,7 +14,7 @@ include/sdsl/suffix_arrays.hpp: sdsl-lite/build/Makefile
+ 	$(MAKE) -C sdsl-lite/build install
+
+ sdsl-lite/build/Makefile:
+-	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../.. ..
++	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+
+
+ $(PROG): $(wildcard *.cpp *.c *.h) ./include/sdsl/suffix_arrays.hpp version.h

recipes/fmsi/0002-version.patch

@@ -0,0 +1,7 @@
+diff --git a/src/version b/src/version
+index ee1372d..abd4105 100644
+--- a/src/version
++++ b/src/version
+@@ -1 +1 @@
+-0.2.2
++${PKG_VERSION}

recipes/fmsi/build.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+	export CXXFLAGS="${CXXFLAGS}"
+fi
+
+make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
+	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \
+	-j"${CPU_COUNT}"
+
+chmod 0755 ${PREFIX}/bin/fmsi

recipes/fmsi/meta.yaml

@@ -0,0 +1,49 @@
+{% set version = "0.2.4" %}
+{% set sha256 = "67c930b8bad30e786fb7a59cc8592e1a7231024debc95af7e2c203bb7022b0b3" %}
+
+package:
+  name: fmsi
+  version: {{ version }}
+
+source:
+  url: https://github.com/OndrejSladky/fmsi/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    - 0001-Makefile.patch
+    - 0002-version.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('fmsi', max_pin="x.x") }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - sdsl-lite
+  run:
+    - sdsl-lite
+
+test:
+  commands:
+    - fmsi -h 2>&1 | grep "FMSI"
+
+about:
+  home: "https://github.com/OndrejSladky/fmsi"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform."
+  dev_url: "https://github.com/OndrejSladky/fmsi"
+  doc_url: "https://github.com/OndrejSladky/fmsi/blob/v{{ version }}/README.md"
+
+extra:
+  identifiers:
+    - doi:10.1101/2024.03.06.583483
+    - doi:10.1101/2023.02.01.526717
+  additional-platforms:
+    - linux-aarch64

recipes/gencove/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.21.0" %}
-{% set sha256 = "805be8b0c0f3e8d189bca16a805649e9594d455c0fa183ecd856ee3208287258" %}
+{% set version = "2.23.0" %}
+{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
 
 package:
   name: {{ name }}