Update orthofinder for 3.0.1b1 beta release (#51202)

* Create orthofinder 3.0.1 beta release * Re-add run_exports --------- Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
bioconda · Oct 7, 2024 · 106a368 · 106a368
1 parent 1bc7f1b
commit 106a368
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Showing 2 changed files with 17 additions and 4 deletions.
diff --git a/recipes/orthofinder/build.sh b/recipes/orthofinder/build.sh
@@ -12,10 +12,17 @@ sed -i.bak 's/raxmlHPC-AVX/raxmlHPC-AVX2/g' scripts_of/config.json
 cp scripts_of/config.json $PREFIX/bin/scripts_of/config.json
 
 cp tools/convert_orthofinder_tree_ids.py $PREFIX/bin/
+cp tools/create_files_for_hogs.py $PREFIX/bin/
 cp tools/make_ultrametric.py $PREFIX/bin/
+cp tools/orthogroup_gene_count.py $PREFIX/bin/
 cp tools/primary_transcript.py $PREFIX/bin/
 
 chmod a+x $PREFIX/bin/orthofinder
 chmod a+x $PREFIX/bin/convert_orthofinder_tree_ids.py
+chmod a+x $PREFIX/bin/create_files_for_hogs.py
 chmod a+x $PREFIX/bin/make_ultrametric.py
+chmod a+x $PREFIX/bin/orthogroup_gene_count.py
 chmod a+x $PREFIX/bin/primary_transcript.py
+
+mkdir -p $PREFIX/share/orthofinder/
+cp -r ExampleData $PREFIX/share/orthofinder/
diff --git a/recipes/orthofinder/meta.yaml b/recipes/orthofinder/meta.yaml
@@ -1,13 +1,13 @@
-{% set version = "2.5.5" %}
-{% set sha256 = "43d034a66a13adba8872a0d4a76e32c25305a7fae638754adb61c37a3f957bd9" %}
+{% set version = "3.0.1b1" %}
+{% set sha256 = "0252560f7ee2303ac3400f130e9eb81b3f6419062aa677642a7258659b43a68c" %}
 
 package:
   name: orthofinder
   version: {{ version }}
 
 build:
   noarch: generic
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('orthofinder', max_pin="x") }}
 
@@ -17,7 +17,7 @@ source:
 
 requirements:
   run:
-    - python >=3.7
+    - python >=3.7,<3.12
     - scipy
     - blast
     # https://github.com/davidemms/OrthoFinder/issues/826 https://github.com/bbuchfink/diamond/issues/707
@@ -32,6 +32,9 @@ requirements:
     - iqtree
     - bzip2
     - mmseqs2
+    - scikit-learn
+    - biopython
+    - aster
 
 test:
   commands:
@@ -42,3 +45,6 @@ about:
   summary: Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!
   license: GPLv3
   license_file: License.md
+
+files:
+  - ExampleData