Merge branch 'master' into bump/starfish

recipes/cosigt/build.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+go mod init cosigt
+go mod tidy
+go get -d ./...
+CGO_ENABLED=0 go build -o $PREFIX/bin/cosigt .

recipes/cosigt/meta.yaml

@@ -0,0 +1,38 @@
+{% set name = "cosigt" %}
+{% set version = "0.1.1" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+      - {{ pin_subpackage(name, max_pin='x.x') }}
+
+source:
+  - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/{{ version }}.tar.gz
+    sha256: 7db68d7e02424fba7248db4ddd0853f1c634b31e62906037765f1f481e63635d
+
+requirements:
+  build:
+    - {{ compiler('go') }}
+
+test:
+  commands:
+    - cosigt -h
+
+about:
+  home: https://github.com/davidebolo1993/{{ name }}
+  license: 'GNU General Public License v3 (GPLv3)'
+  license_family: GPL3
+  license_file: LICENSE
+  summary: Cosigt (COsine SImilarity-based GenoTyper)
+  dev_url: https://github.com/davidebolo1993/{{ name }}
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - AndreaGuarracino

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/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/hmftools-esvee/meta.yaml

@@ -1,17 +1,18 @@
 {% set version = "1.0_beta" %}
-{% set sha256 = "7ee885d48306e73c0cefacd7d59f2aabd213fc6d78d4ca8489a8d6c25e8ce333" %}
+{% set beta_suffix = ".2" %}
+{% set sha256 = "75933500cde12741534580d84bdafc6ad7b3290f382973dbcf540580b9453bd9" %}
 
 package:
   name: hmftools-esvee
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/esvee-v{{ version }}/esvee_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/esvee-v{{ version }}/esvee_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}
 

recipes/hmftools-linx/meta.yaml

@@ -1,12 +1,13 @@
-{% set version = "1.25" %}
-{% set sha256 = "2fa9a91801239ded3e82fcd0ee9987e6181d0e400855420ef7f5000f3b4a96da" %}
+{% set version = "2.0_beta" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "34bb84e9563d3847544f5e457211ff9a74473131e5a609ebae960a7a3cfcf8d9" %}
 
 package:
   name: hmftools-linx
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/linx-v{{ version }}/linx_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/linx-v{{ version }}/linx_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
@@ -26,6 +27,7 @@ requirements:
     - r-magick
     - bioconductor-gviz
     - circos >=0.69.6
+    - perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD)
 
 test:
   commands:

recipes/hmftools-purple/meta.yaml

@@ -1,12 +1,13 @@
-{% set version = "4.0.2" %}
-{% set sha256 = "fb534734b4a0833c8d68591e009caea5b654714211a95f23570c1fca9bfa57a9" %}
+{% set version = "4.1_beta" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "aa5b1ec3c0e67027750fce6ac71bc31d55c37405c8e00571594d58c837e74a51" %}
 
 package:
   name: hmftools-purple
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/purple-v{{ version }}/purple_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/purple-v{{ version }}/purple_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
@@ -21,6 +22,7 @@ requirements:
     - openjdk >=8
     - xorg-libxtst
     - circos >=0.69.6
+    - perl-gd >=2.76 # Fixes missing GD perl module error (even though circos does install GD)
     - bioconductor-variantannotation
     - r-cairo
     - r-cowplot

recipes/hmftools-redux/meta.yaml

@@ -1,17 +1,18 @@
 {% set version = "1.0_beta" %}
-{% set sha256 = "40caa3f1f493a1eb3c0e029f084f3c7d52456dbd9bbc72f118015b525ea9d467" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "0789230f3f7c8fe65c26709fbe4bc95a70e8b7465526dac8c1613d632c43a1e8" %}
 
 package:
   name: hmftools-redux
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/redux-v{{ version }}/redux_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/redux-v{{ version }}/redux_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
 

recipes/meta_eukaryome_detect/meta.yaml

@@ -0,0 +1,48 @@
+{% set name = "meta_eukaryome_detect" %}
+{% set version = "0.1.1" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: 0199ad179d36d3683b8122f41b1e5db6c5d7d94324c3fe5187d576fafdfa2cdc
+
+build:
+  number: 0
+  entry_points:
+    - meta_eukaryome_detect = meta_eukaryome_detect.meta_eukaryome_detect:main
+  script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps"
+  noarch: python
+  run_exports:
+    {{ pin_subpackage(name, max_pin="x") }}
+
+requirements:
+  host:
+    - pip
+    - python >=3.11
+    - poetry
+  run:
+    - ngless
+    - samtools
+    - pandas >=2.0
+    - requests
+test:
+  imports:
+    - meta_eukaryome_detect
+  commands:
+    - meta_eukaryome_detect --help
+
+about:
+  home: "https://github.com/grp-bork/meta_eukaryome_detect"
+  license: "MIT License"
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Pathogen, Parasite, Eukaryote and Virus detection in metagenomes."
+  doc_url: "https://grp-bork.embl-community.io/grp-microbiome-astrology/meta_eukaryome_detect/"
+  dev_url: "https://github.com/grp-bork/meta_eukaryome_detect"
+
+extra:
+  recipe-maintainers:
+    - fullama

recipes/openms-meta/meta.yaml

@@ -12,11 +12,11 @@ source:
 {% else %}
 source:
   url: https://github.com/OpenMS/OpenMS/releases/download/release%2F3.2.0/OpenMS-3.2.tar.gz # since we discarded the trailing 0 during the GHA we have to hard code this, fix it next release
-  md5: 60ebfe8a45f7e1fb5566d21231b460e8
+  md5: e15b34a4ccaf7070d186fd01a6d57f3e
 {% endif %}
 
 build:
-  number: 4
+  number: 5
   skip: True  # [osx]
 
 # Try this when building with GUI
@@ -39,7 +39,7 @@ requirements:
       - libtool
       - xerces-c
       - boost-cpp
-      - eigen >=3.3.2
+      - eigen >=3.3.4
       - hdf5 >=1.10
       - bzip2
       - qt-main
@@ -71,7 +71,7 @@ outputs:
           - libtool
           - xerces-c
           - boost-cpp
-          - eigen >=3.3.2
+          - eigen >=3.3.4
           - hdf5 >=1.10
           - bzip2
           - qt-main
@@ -114,7 +114,7 @@ outputs:
         - libtool
         - xerces-c
         - boost-cpp
-        - eigen >=3.3.2
+        - eigen >=3.3.4
         - hdf5 >=1.10
         - bzip2
         - qt-main

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: