Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 2 commits into from
Dec 6, 2024
Merged
Changes from 1 commit
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
@@ -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)
Original file line number Diff line number Diff line change
@@ -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 \
1 change: 1 addition & 0 deletions snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py
Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
@@ -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

40 changes: 4 additions & 36 deletions snappy_wrappers/wrappers/gcnv/environment.yaml
Original file line number Diff line number Diff line change
@@ -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
Original file line number Diff line number Diff line change
@@ -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}
Original file line number Diff line number Diff line change
@@ -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}
4 changes: 2 additions & 2 deletions snappy_wrappers/wrappers/gcnv/preprocess_intervals/wrapper.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
# isort:skip_file
from snappy_pipeline.utils import DictQuery
import os
#from snappy_pipeline.utils import DictQuery
#import os
tedil marked this conversation as resolved.
Show resolved Hide resolved

from snakemake.shell import shell

Loading