feat: Update GCNV environment to 0.9 kernel and GATK4.6.1 (#557)

Co-authored-by: Nicolai von Kügelgen <[email protected]>
bihealth · Dec 6, 2024 · 7239fd0 · 7239fd0
1 parent 625187b
commit 7239fd0
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Showing 8 changed files with 10 additions and 38 deletions.
diff --git a/snappy_wrappers/wrappers/gcnv/call_cnvs_case_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/call_cnvs_case_mode/wrapper.py
@@ -17,6 +17,7 @@
 export MKL_NUM_THREADS=16
 export OMP_NUM_THREADS=16
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 # Force full replacement of previous results
 # (this also solves issues when gatk tries to shutil copy file ownership)

diff --git a/snappy_wrappers/wrappers/gcnv/call_cnvs_cohort_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/call_cnvs_cohort_mode/wrapper.py
@@ -21,6 +21,7 @@
 export MKL_NUM_THREADS=16
 export OMP_NUM_THREADS=16
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 gatk GermlineCNVCaller \
     --run-mode COHORT \

diff --git a/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py b/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py
@@ -42,6 +42,7 @@
 export MKL_NUM_THREADS={snakemake.threads}
 export OMP_NUM_THREADS={snakemake.threads}
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 # Get contig name style
 egrep "^@SQ\s+SN:chr[0-9XY]{{1,2}}\s+" {snakemake.input.interval_list} > /dev/null && true

diff --git a/snappy_wrappers/wrappers/gcnv/contig_ploidy_case_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/contig_ploidy_case_mode/wrapper.py
@@ -36,6 +36,7 @@
 shell(
     r"""
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 set -x
 

diff --git a/snappy_wrappers/wrappers/gcnv/environment.yaml b/snappy_wrappers/wrappers/gcnv/environment.yaml
@@ -3,40 +3,8 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - gatk4==4.3.0.0
-  - bcftools==1.10.2
-  - htslib==1.10.2
+  - gatk4==4.6.1.0
+  - bcftools
+  - htslib
   - parallel==20240122
-  # the hard to install gcnvkernel
-  - gcnvkernel==0.8
-  # gcnvkernel dependencies
-  - python==3.6.10
-  - pip==21.3.1
-  - mkl==2019.5
-  - mkl-service==2.3.0
-  - numpy==1.17.5
-  - theano==1.0.4
-  - tensorflow==1.10.0
-  - scipy==1.0.0
-  - pymc3==3.1
-  - joblib==1.2.0
-  - h5py==2.10.0
-  - keras==2.2.4
-  - intel-openmp==2022.1.0
-  - scikit-learn==0.23.1
-  - matplotlib==3.2.1
-  - pandas==1.0.3
-  - typing_extensions==4.1.1
-  - dill==0.3.4
-  - r-base==3.6.2
-  - r-data.table==1.12.8
-  - r-dplyr==0.8.5
-  - r-getopt==1.20.3
-  - r-ggplot2==3.3.0
-  - r-gplots==3.0.3
-  - r-gsalib==2.1
-  - r-optparse==1.6.4
-  - r-backports==1.1.10
-  - biopython==1.76
-  - pyvcf==0.6.8
-  - pysam==0.15.3
+  - gcnvkernel==0.9
diff --git a/snappy_wrappers/wrappers/gcnv/post_germline_calls/wrapper.py b/snappy_wrappers/wrappers/gcnv/post_germline_calls/wrapper.py
@@ -13,6 +13,7 @@
 trap "rm -rf $TMPDIR" ERR EXIT
 
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 itv_vcf={snakemake.output.itv_vcf}
 seg_vcf={snakemake.output.seg_vcf}

diff --git a/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py b/snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/wrapper.py
@@ -13,6 +13,7 @@
 trap "rm -rf $TMPDIR" ERR EXIT
 
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
 
 itv_vcf={snakemake.output.itv_vcf}
 seg_vcf={snakemake.output.seg_vcf}

diff --git a/snappy_wrappers/wrappers/gcnv/preprocess_intervals/wrapper.py b/snappy_wrappers/wrappers/gcnv/preprocess_intervals/wrapper.py
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 # isort:skip_file
-from snappy_pipeline.utils import DictQuery
-import os
 
 from snakemake.shell import shell
-Original file line number
+Diff line change
@@ Expand Up / @@ -36,6 +36,7 @@ @@
     shell(
         r"""
     export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
+    export PYTENSOR_FLAGS="base_compiledir=$TMPDIR/pytensor_compile_dir"
     set -x
@@ Expand Down @@