Update somaticseq to 3.9.1 (bioconda#52489)

* Update somaticseq to 3.9.0 * Update somaticseq to 3.9.1 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]>
mencian · Dec 2, 2024 · 0d41c43 · 0d41c43
1 parent 12f784b
commit 0d41c43
Showing 1 changed file with 28 additions and 7 deletions.
diff --git a/recipes/somaticseq/meta.yaml b/recipes/somaticseq/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "somaticseq" %}
-{% set version = "3.8.0" %}
-{% set sha256 = "d936bab4b042ce6f7e13420fda747c264e4047be9e1ed0186c2379a74f526412" %}
+{% set version = "3.9.1" %}
+{% set sha256 = "309985d4fbf7ae3cba8dc900f5dd01ac7605f09d662d3d643e9804a4ce977c79" %}
 
 package:
   name: {{ name|lower }}
@@ -13,16 +13,36 @@ source:
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  entry_points:
+    - somaticseq = somaticseq.somaticseq_parallel:main
+    - somaticseq_parallel = somaticseq.somaticseq_parallel:main
+    - somaticseq_xgboost = somaticseq.somatic_xgboost:main
+    - somaticseq_tsv2vcf = somaticseq.somatic_tsv2vcf:main
+    - somaticseq_single_vcf2tsv = somaticseq.single_sample_vcf2tsv:main
+    - somaticseq_paired_vcf2tsv = somaticseq.somatic_vcf2tsv:main
+    - somaticseq_concat = somaticseq.genomic_file_parsers.concat:main
+    - somaticseq_linguistic_sequence_complexity = somaticseq.utilities.linguistic_sequence_complexity:main
+    - somaticseq_loci_counter = somaticseq.utilities.lociCounterWithLabels:main
+    - somaticseq_paired_end_bam2fastq = somaticseq.utilities.paired_end_bam2fastq:main
+    - somaticseq_split_bed_into_equal_regions = somaticseq.utilities.split_bed_into_equal_regions:main
+    - somaticseq_make_alignment_scripts = somaticseq.utilities.dockered_pipelines.makeAlignmentScripts:main
+    - somaticseq_make_somatic_scripts = somaticseq.utilities.dockered_pipelines.makeSomaticScripts:main
+    - somaticseq_run_workflows = somaticseq.utilities.dockered_pipelines.run_workflows:main
+    - somaticseq_split_vcf = somaticseq.vcf_modifier.splitVcf:main
   run_exports:
     - {{ pin_subpackage('somaticseq', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3
+    - python >=3.11
     - pip
+    - setuptools-scm
+    - setuptools
   run:
-    - python >=3
+    - python >=3.11
     - numpy
     - pysam
     - scipy
@@ -48,11 +68,12 @@ test:
     - makeSomaticScripts.py --help
 
 about:
-  home: https://bioinform.github.io/somaticseq/
+  home: https://bioinform.github.io/somaticseq
   license: BSD-2-Clause
   license_file: LICENSE.txt
   license_family: BSD
-  summary: An ensemble approach to accurately detect somatic mutations
+  summary: "An ensemble approach to accurately detect somatic mutations."
+  dev_url: https://github.com/bioinform/somaticseq
   description: >
     SomaticSeq is an ensemble caller that has the ability to use machine learning to filter out false positives.
     The detailed documentation is included in the package, located in docs/Manual.pdf. A quick guide can also be found here.