[MISC] Create conda samtools environment

Signed-off-by: Lydia Buntrock <[email protected]>
seqan · Oct 26, 2022 · 91dad04 · 91dad04
1 parent c850899
commit 91dad04
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Showing 7 changed files with 21 additions and 7 deletions.
diff --git a/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk b/test/benchmark/caller_comparison_iGenVar_only/workflow/rules/callers.smk
@@ -105,5 +105,7 @@ rule picard:
         vcf = "results/caller_comparison_iGenVar_only/{input_combination}/variants.vcf"
     log:
         "logs/caller_comparison_iGenVar_only/picard_output.{input_combination}.log"
+    conda:
+        "../../../envs/simulation.yaml"
     shell:
         "picard SortVcf -I {input.vcf} -O {output.vcf} -Xms1g -Xmx100g --TMP_DIR tmp/picard/ &>> {log}"
diff --git a/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk b/test/benchmark/caller_comparison_long_read/workflow/rules/callers.smk
@@ -84,6 +84,8 @@ rule picard:
         vcf = "results/caller_comparison_long_read/{dataset}/SVIM/variants.vcf"
     log:
         "logs/caller_comparison_long_read/SVIM/picard_output.{dataset}.log"
+    conda:
+        "../../../envs/simulation.yaml"
     shell:
         "picard SortVcf -I {input.vcf} -O {output.vcf} -Xms1g -Xmx100g --TMP_DIR tmp/picard/ &>> {log}"
         # The Xms and Xmx sets the java memory for avoiding "java.lang.OutOfMemoryError: GC overhead limit exceeded"

diff --git a/test/benchmark/envs/environment.yml b/test/benchmark/envs/environment.yml
@@ -4,15 +4,13 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # - bedops           # for vcf2bed
   - bgzip            # rule tabix - accepts only zipped files zipped with bgzip
   - crossmap         # for coordinate_conversion.sh
   - delly=1.0.3
   # - lumpy-sv=0.3.1   # rule run_Lumpy
   - mamba
   - matplotlib       # rule run_svim
   - pbsv=2.6.2
-  - picard           # rule picard
   - pip
   - python=3.6
   - r

diff --git a/test/benchmark/envs/samtools.yaml b/test/benchmark/envs/samtools.yaml
@@ -1,5 +1,6 @@
+name: samtools
 channels:
  - bioconda
-#Sorting BAM files from NGMLR fails in samtools version>=1.10, therefore fix to version 1.9
+# Sorting BAM files from NGMLR fails in samtools version>=1.10, therefore fix to version 1.9
 dependencies:
- - samtools=1.9
+ - samtools #=1.9
diff --git a/test/benchmark/envs/simulation.yaml b/test/benchmark/envs/simulation.yaml
@@ -0,0 +1,10 @@
+name: simulation
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - bwa>=0.7  # for aligning the simulated reads
+  - mamba
+  - mason     # for simulation Illumina short reads
+  - picard    # for sorting vcf files
diff --git a/test/benchmark/prepare_BAM_with_crossmap.sh b/test/benchmark/prepare_BAM_with_crossmap.sh
@@ -12,6 +12,9 @@ wget --retry-connrefused --waitretry=30 --read-timeout=30 --timeout=30 --tries=2
 
 echo "$(tput setaf 1)$(tput setab 7)------- CrossMap installed and prepared (5.1/9.6) --------$(tput sgr 0)" 1>&3
 
+conda env create -f Repos/iGenVar/test/benchmark/envs/samtools.yaml
+conda activate samtools
+
 # Illumina Mate Pair
 ## prepare reference file:
 ## reorder reference:
@@ -78,6 +81,6 @@ CrossMap.py bam hg19ToHg38.over.chain.gz long_reads/GRCh37/NA24385_phased_possor
     long_reads/GRCh38/NA24385_phased_possorted_bam.Hg38.bam
 CrossMap.py bam hg19ToHg38.over.chain.gz long_reads/GRCh37/NA24385_phased_possorted_bam.md.bam \
     long_reads/GRCh38/NA24385_phased_possorted_bam.md.Hg38.bam
-conda activate benchmarks
+conda activate iGenVar_benchmark
 
 echo "$(tput setaf 1)$(tput setab 7)------- BAM files prepared (5.3/9.6) --------$(tput sgr 0)" 1>&3
diff --git a/test/benchmark/prepare_truth_set_with_NCBI.sh b/test/benchmark/prepare_truth_set_with_NCBI.sh
@@ -74,6 +74,4 @@ CrossMap.py bed hg19ToHg38.over.chain.gz truth_set/${TRUTH_SET}.renamed_chr.bed
 # remove chr from chromosome names again
 sed -e 's!chr!!' truth_set/${TRUTH_SET}.renamed_chr.Hg38.bed > truth_set/${TRUTH_SET}.Hg38.bed
 
-# convert2bed --input=vcf --insertions < NA24385.GRCh38.large_svs.vcf.gz > insertions.bed
-
 echo "$(tput setaf 1)$(tput setab 7)------- truth set files prepared (5.6/9.6) --------$(tput sgr 0)" 1>&3