From 8647ce3add20cccad60e77245d27217788ccd668 Mon Sep 17 00:00:00 2001
From: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
Date: Wed, 27 Apr 2022 12:22:08 +0200
Subject: [PATCH] [BENCHMARK] Install Delly2, GRIDSS and TIDDIT

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
---
 test/benchmark/envs/environment.yml           | 21 +++++++++++--------
 test/benchmark/envs/gridss.yaml               |  8 +++++++
 .../iGenVar_run_benchmark.sh                  |  2 +-
 test/benchmark/prepare_BAM_with_crossmap.sh   |  3 +++
 4 files changed, 24 insertions(+), 10 deletions(-)
 create mode 100644 test/benchmark/envs/gridss.yaml

diff --git a/test/benchmark/envs/environment.yml b/test/benchmark/envs/environment.yml
index d318c027..151d5667 100644
--- a/test/benchmark/envs/environment.yml
+++ b/test/benchmark/envs/environment.yml
@@ -1,25 +1,28 @@
-name: iGenVar_benchmark
+name: benchmarks
 channels:
   - defaults
   - conda-forge
   - bioconda
 dependencies:
-  # - bedops    # for vcf2bed
-  - bgzip       # rule tabix - accepts only zipped files zipped with bgzip
-  - crossmap    # for coordinate_conversion.sh
+  # - 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
+  - matplotlib       # rule run_svim
   - pbsv=2.6.2
-  - picard      # rule picard
+  - picard           # rule picard
   - pip
   - python=3.6
   - r
   - r-tidyverse
-  - samtools
-  - scipy       # rule run_svim
-  - snakemake
+  - samtools         # bgzip for rule tabix - accepts only zipped files zipped with bgzip
+  - scipy            # rule run_svim
+  - snakemake=6.15.5 # snakemake>6 needs python>3.6
   # - svim=2.0.0
   - tabix
+  - tiddit=2.12.1    # rule run_TIDDIT
   - yappi
   - pip:
     - truvari
diff --git a/test/benchmark/envs/gridss.yaml b/test/benchmark/envs/gridss.yaml
new file mode 100644
index 00000000..81232b85
--- /dev/null
+++ b/test/benchmark/envs/gridss.yaml
@@ -0,0 +1,8 @@
+name: gridss
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - gridss=2.13.2   # rule run_GRIDSS
+  # Python 3.10.4
diff --git a/test/benchmark/parameter_benchmarks/iGenVar_run_benchmark.sh b/test/benchmark/parameter_benchmarks/iGenVar_run_benchmark.sh
index eead516c..f6de36da 100755
--- a/test/benchmark/parameter_benchmarks/iGenVar_run_benchmark.sh
+++ b/test/benchmark/parameter_benchmarks/iGenVar_run_benchmark.sh
@@ -22,7 +22,7 @@ start=$(date +%s) # get starting date
 # conda env create -f environment.yml
 
 # source ~/.bashrc                  # if the .bashrc is not executed automatically
-conda activate iGenVar_benchmark
+conda activate benchmarks
 
 # -------- -------- run iGenVar with default values -------- -------- #
 
diff --git a/test/benchmark/prepare_BAM_with_crossmap.sh b/test/benchmark/prepare_BAM_with_crossmap.sh
index 27e8ba29..5f529d83 100644
--- a/test/benchmark/prepare_BAM_with_crossmap.sh
+++ b/test/benchmark/prepare_BAM_with_crossmap.sh
@@ -17,6 +17,9 @@ echo "$(tput setaf 1)$(tput setab 7)------- CrossMap installed and prepared (5.1
 ## reorder reference:
 samtools faidx data/reference/GRCh37/hg19.fa $(cat Repos/iGenVar/test/benchmark/data/order_of_hg19.txt) \
     > data/reference/GRCh37/hg19.reordered.fa
+## for GRIDSS:
+less data/reference/GRCh37/hg19.reordered.fa | sed -n -e '/>chrM/,$p' | sed -e '/>chr1_gl000191_random/,$d' > data/reference/GRCh37/hg19.reordered.short.fa
+less data/reference/GRCh37/hg19.reordered.fa | sed -e '/>chrM/,$d' >> data/reference/GRCh37/hg19.reordered.short.fa
 
 echo "$(tput setaf 1)$(tput setab 7)------- reference files prepared (5.2/9.6) --------$(tput sgr 0)" 1>&3