Update lorikeet-genome version v0.8.2 (bioconda#44654)

* chore: update lorikeet version and recipe * fix: fix linting issues by removing pip section * fix: remove lorikeet from blacklist as associated error is fixed * fix: pinned subpackage error * fix: package name and folder matching * fix: sha256 correction * fix: change install path * fix: python version must be the same at runtime * fix: python version must be compatible with scikit-allel --------- Co-authored-by: Thanh Lee <[email protected]>
mencian · Dec 8, 2023 · de93d8d · de93d8d
1 parent 2ca1a67
commit de93d8d
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Showing 3 changed files with 27 additions and 35 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -357,9 +357,6 @@ recipes/conduit-assembler
 recipes/metabat2
 recipes/bcftools-snvphyl-plugin
 
-# error: no matching package named `bird_tool_utils` found location searched: https://github.com/wwood/galah#8440eeb8 required by package `galah v0.3.1 (https://github.com/wwood/galah#8440eeb8)` ... which satisfies git dependency `galah` of package `lorikeet-genome v0.7.3
-recipes/lorikeet-genome
-
 # rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp'
 recipes/kinsimriboswitch
 

diff --git a/recipes/lorikeet-genome/build.sh b/recipes/lorikeet-genome/build.sh
@@ -12,4 +12,4 @@ C_INCLUDE_PATH=$PREFIX/include \
 LIBRARY_PATH=$PREFIX/lib \
 LIBCLANG_PATH=$PREFIX/lib/libclang.so \
 OPENSSL_DIR=$PREFIX \
-cargo install --force --root $PREFIX
+cargo install --path ./ --force --root $PREFIX
diff --git a/recipes/lorikeet-genome/meta.yaml b/recipes/lorikeet-genome/meta.yaml
@@ -1,62 +1,57 @@
-{% set version = "0.7.3" %}
-{% set name = "lorikeet" %}
-{% set sha256 = "663e53c2451e06af3334b612a7518180fa528e2d12ebe869f74f78996e2a82a5" %}
+{% set version = "0.8.2" %}
+{% set name = "lorikeet-genome" %}
+{% set sha256 = "125fb87f7aa586aa92183ed2c11721477d0b2ba2481f80a1e047ab581e3ff50b" %}
 
 package:
-  name: lorikeet-genome
+  name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 source:
-  url: https://github.com/rhysnewell/{{ name }}/archive/v{{ version }}.tar.gz
+  url: https://github.com/rhysnewell/lorikeet/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
   build:
-    - rust >=1.40
-    - python >=3.9
+    - rust >=1.70
+    - python ==3.10
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - perl
     - pkg-config
     - make
     - cmake
   host:
     - zlib
-    - gsl
+    - blis
     - libblas
+    - openblas
     - openssl
-    - htslib
+    - clangdev
   run:
-    - python >=3.9
-    - htslib
-    - parallel
-    - numpy
-    - matplotlib-base
+    - samtools >=1.9
+    - coreutils
+    - python ==3.10
     - prodigal
+    - minimap2 >=2.24
+    - bwa >=0.7.17
+    - bwa-mem2
+    - numpy
+    - scikit-allel >=1.3.6
     - svim
-    - samtools >=1.9
     - bcftools
-    - vt
-    - zlib
-    - gsl
-    - starcode
-    - bwa >=0.7.17
-    - bwa-mem2 >=2.2.1
-    - minimap2
-    - fastani
-    - dashing
-    - ngmlr
-    - scikit-allel
-    - polars
-    - scipy
+    - pip
+    - polars >=0.18
+    - scipy >=1.11
+    - cmake >=3.21
 
 test:
   commands:
-    - {{ name }} --version | grep '{{ version }}'
+    - lorikeet --version | grep '{{ version }}'
 
 about:
   home: https://github.com/rhysnewell/Lorikeet