Merge branch 'master' into Xiangyang1984-patch-11

recipes/cosigt/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "cosigt" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 
 package:
   name: {{ name }}
@@ -11,8 +11,8 @@ build:
       - {{ pin_subpackage(name, max_pin='x.x') }}
 
 source:
-  - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/{{ version }}.tar.gz
-    sha256: 7db68d7e02424fba7248db4ddd0853f1c634b31e62906037765f1f481e63635d
+  - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/v{{ version }}.tar.gz
+    sha256: 8cd92c395643720492cc1626d16aa5258bf44a6f448c2ea3407a257bf0ab6416
 
 requirements:
   build:

recipes/devider/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -euo
+
+# 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"
+
+# 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 .
+cp scripts/* $PREFIX/bin

recipes/devider/meta.yaml

@@ -0,0 +1,47 @@
+{% set version="0.0.1" %}
+
+package:
+  name: devider
+  version: {{ version }}
+
+source:
+  url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
+  sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('devider', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+    - {{ compiler('rust') }} 
+    - cargo-bundle-licenses
+    - make
+    - cmake >=3.12
+  run:
+    - python 
+    - samtools
+    - minimap2
+    - lofreq >=2.1.5
+    - tabix
+    - pysam >=0.16
+
+test:
+  commands:
+    - devider -h
+    - run_devider_pipeline -h
+    - haplotag_bam -h
+
+about:
+  home: https://github.com/bluenote-1577/devider
+  license: MIT
+  license_file:
+    - LICENSE
+    - THIRDPARTY.yml 
+  summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
+
+extra:
+  recipe-maintainers:
+    - bluenote-1577

recipes/fastk/build.sh

@@ -1,16 +1,19 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="-L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 export CFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 export CPPFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib"
 
 # build HTSLIB
 cd HTSLIB
-make lib-static
+make -j"${CPU_COUNT}" lib-static
 cd -
 # build LIBDEFLATE
 cd LIBDEFLATE
-make
+make -j"${CPU_COUNT}"
 cd -
 # build fastk
-make
+make -j"${CPU_COUNT}"
 make install

recipes/fastk/meta.yaml

@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 0
+  number: 1
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("fastk", max_pin="x") }}
@@ -36,3 +36,7 @@ about:
   license: https://github.com/thegenemyers/FASTK/blob/master/LICENSE
   summary: FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
   home: https://github.com/thegenemyers/FASTK
+
+extra:
+  additional-platforms:
+    - linux-aarch64

recipes/gafpack/build.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -euo
+
+set -xe
+
+# build statically linked binary with Rust
+export RUST_BACKTRACE=1
+cargo install --verbose --path . --root ${PREFIX} --no-track

recipes/gafpack/meta.yaml

@@ -0,0 +1,38 @@
+{% set name = "gafpack" %}
+{% set version = "0.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 0b78d8047132965c7b0a9b0f3dc26682c1251d08507ebdd98583d9c1b563c758 
+
+build:
+  number: 0
+  run_exports:
+      - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+
+test:
+  commands:
+    - gafpack --help
+
+about:
+  home: https://github.com/pangenome/{{ name }}
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Convert alignments to pangenome variation graphs to coverage maps
+  dev_url: https://github.com/pangenome/{{ name }}
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - AndreaGuarracino

recipes/gnparser/build.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -xe
+
 cd gnparser
 CGO_ENABLED=0
 go clean

recipes/gnparser/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('gnparser', max_pin="x") }}
 
@@ -34,5 +34,8 @@ about:
 
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   identifiers:
     - doi:https://doi.org/10.5281/zenodo.5111569

recipes/longcallr_nn/meta.yaml

@@ -0,0 +1,51 @@
+{% set name = "longcallr_nn" %}
+{% set version = "0.0.1" %}
+{% set hash = "294155357b7165b127fc821b06dcdbeee28c108a0caf442b28992a5a5cc3e583" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://github.com/huangnengCSU/longcallR-nn/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: {{ hash }}
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - longcallR_nn=longcallR_nn.longcallR_nn:main
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+requirements:
+  host:
+    - pip
+    - python 3.9.*
+  run:
+    - python 3.9.*
+    - numpy 1.21.0
+    - pyyaml
+    - pysam
+    - tensorboardX
+    - pytorch 1.13.*
+    - torchvision
+    - torchmetrics
+
+test:
+  commands:
+    - longcallR_nn --help
+
+about:
+  home: "https://github.com/huangnengCSU/longcallR-nn"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model."
+  dev_url: "https://github.com/huangnengCSU/longcallR-nn"
+
+extra:
+  recipe-maintainers:
+    - huangnengCSU

recipes/merquryfk/build.sh

@@ -1,8 +1,11 @@
 #!/bin/bash
+
+set -xe
+
 export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make
+make -j"${CPU_COUNT}"
 mkdir -p $PREFIX/bin
 
 cp HAPmaker  $PREFIX/bin

recipes/merquryfk/meta.yaml

@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage("merquryfk", max_pin="x") }}
@@ -50,3 +50,7 @@ about:
   license: https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE
   summary: MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses.
   home: https://github.com/thegenemyers/MERQURY.FK
+
+extra:
+  additional-platforms:
+    - linux-aarch64

recipes/meta_eukaryome_detect/meta.yml → recipes/meta_eukaryome_detect/meta.yaml

@@ -22,10 +22,11 @@ requirements:
   host:
     - pip
     - python >=3.11
+    - poetry
   run:
     - ngless
     - samtools
-    - pandas >= 2.0
+    - pandas >=2.0
     - requests
 test:
   imports:

recipes/metabolights-utils/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.1.11" %}
+{% set version = "1.1.12" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: 5290c8c269f5ec3c55d5fc5b24c014c815b24391b831af528a0bec0545337e7e
+  sha256: a9f482e77df79e1efa6c4884edd9b66f21ac7267cf2d8aa7bf9c018cc9c08788
 
 build:
   entry_points:

recipes/oakvar/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.11" %}
-{% set sha256 = "16ac185b5e26e422111f7d7e568bd602e972ac2a91feeb4ee61a2193d47cd9a7" %}
+{% set version = "2.11.12" %}
+{% set sha256 = "eb979f31a9291c8285d0ec335102455e8ad0210f59ffddf8074b1fabf76061a3" %}
 
 package:
   name: {{ name|lower }}

recipes/perl-excel-writer-xlsx/meta.yaml

@@ -1,16 +1,18 @@
 {% set name = "perl-excel-writer-xlsx" %}
-{% set version = "1.11" %}
-{% set sha256 = "cb3300d23119c698864ef0b73c19a72cba718bfc06ed007359a5313f961cc2a0" %}
+{% set version = "1.13" %}
+{% set sha256 = "3d60b14e40cd6d93b8e5b40c1bf814122301107fe10e7e6b4120ed3fe87009c9" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.11.tar.gz
+  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.13.tar.gz
   sha256: {{ sha256 }}
 
 build:
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
   number: 0
   noarch: generic
 

recipes/perl-namespace-autoclean/meta.yaml

@@ -1,17 +1,19 @@
 {% set name = "perl-namespace-autoclean" %}
-{% set version = "0.29" %}
-{% set sha256 = "45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804" %}
+{% set version = "0.31" %}
+{% set sha256 = "d3b32c82e1d2caa9d58b8c8075965240e6cab66ab9350bd6f6bea4ca07e938d6" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/namespace-autoclean-0.29.tar.gz
+  url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/namespace-autoclean-0.31.tar.gz
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:

recipes/pneumo-typer/meta.yaml

@@ -1,5 +1,6 @@
 {% set name = "pneumo-typer" %}
 {% set version = "1.0.2" %}
+
 {% set sha256 = "7f7e224ea5c13256a0597d981207147d1233b45581d11a71c1dd8ef99f14dbf4" %}
 
 package:

recipes/r-archr/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+${R} CMD INSTALL --build . ${R_ARGS}