added version info for rockdb.yaml file

pipelines/annotations.snakefile

@@ -358,18 +358,19 @@ rule merge_annotations:
         deepripe_hg2=anno_dir
         / (source_variant_file_pattern + "_variants.eclip_hg2_deepripe.csv.gz"),
         variant_file=variant_file,
+        vcf_file= anno_tmp_dir / (source_variant_file_pattern + "_variants.vcf"),
     output:
         anno_dir / f"{source_variant_file_pattern}_merged.parquet",
+    resources: mem_mb=10_000 ##!TODO:remove
     shell:
         (
             "HEADER=$(grep  -n  '#Uploaded_variation' "
             + "{input.vep}"
             + "| head | cut -f 1 -d ':') && python "
             + f"{annotation_python_file} "
-            + "merge-annotations $(($HEADER-1)) {input.vep} {input.deepripe_parclip} {input.deepripe_hg2} {input.deepripe_k5} {input.variant_file} {output}"
+            + "merge-annotations $(($HEADER-1)) {input.vep} {input.deepripe_parclip} {input.deepripe_hg2} {input.deepripe_k5} {input.variant_file} {input.vcf_file} {output}"
         )
 
-
 rule deepSea_PCA:
     input:
         deepsea_anno = str(anno_dir / "all_variants.wID.deepSea.parquet")

pipelines/resources/environment_spliceai_rocksdb.yaml

@@ -2,21 +2,21 @@ name: spliceai-rocksdb
 channels:
   - conda-forge
 dependencies:
-  - python>=3.6
-  - python-rocksdb>=0.7
-  - rocksdb
-  - tensorflow-gpu>=2.4
-  - cudnn
-  - cudatoolkit>=11.0
-  - pyarrow
-  - tqdm
-  - pip
-  - setuptools
-  - click
-  - pooch
-  - bioconda::snakemake>=6.1
-  - bioconda::kipoiseq
-  - bioconda::spliceai
-  - bioconda::cyvcf2
+  - python==3.9.15
+  - python-rocksdb==0.7.0
+  - rocksdb==6.13.3
+  - tensorflow-gpu==2.6.2
+  - cudnn==8.8.0.121
+  - cudatoolkit==11.0.3
+  - pyarrow==6.0.1
+  - tqdm==4.65.0
+  - pip==23.2.1
+  - setuptools==68.0.0
+  - click==8.1.6
+  - pooch==1.7.0
+  - bioconda::snakemake==7.31.0
+  - bioconda::kipoiseq==0.7.1
+  - bioconda::spliceai==1.3.1
+  - bioconda::cyvcf2==0.30.16
   - pip:
-    - git+https://github.com/gagneurlab/spliceai_rocksdb.git@master
+    - git+https://github.com/gagneurlab/spliceai_rocksdb.git@0.0.1