Commit 2ce79507 authored by Leon Mei's avatar Leon Mei

changes made today to run on SHARK

parent 95f7f7ff
...@@ -62,7 +62,7 @@ rule report_pipeline: ...@@ -62,7 +62,7 @@ rule report_pipeline:
genes_rubic="Reports/Genes_RUBIC.txt", genes_rubic="Reports/Genes_RUBIC.txt",
venn="Reports/Venn_overlap_genes.png", venn="Reports/Venn_overlap_genes.png",
swarmplot="Reports/Comparison_sizes.png", swarmplot="Reports/Comparison_sizes.png",
circos="Circos/RecurrentRegions_legend.png", #FIXME circos="Circos/RecurrentRegions_legend.png",
go="GO/comparison.txt" go="GO/comparison.txt"
output: output:
html="PipelineResults.html" html="PipelineResults.html"
...@@ -76,7 +76,7 @@ rule report_pipeline: ...@@ -76,7 +76,7 @@ rule report_pipeline:
- Report on segmentation file: seg_ - Report on segmentation file: seg_
- Report on comparison between tools and overlapping regions: tools_ - Report on comparison between tools and overlapping regions: tools_
- Table with all recurrent regions and overlapping genes: table_regions_ - Table with all recurrent regions and overlapping genes: table_regions_
- Circos plot showing the raw segmentation file and recurrent regions detected by both tools: circos_ #FIXME - Circos plot showing the raw segmentation file and recurrent regions detected by both tools: circos_
- Venn diagram showing the overlap between gene lists from both tools: venn_ - Venn diagram showing the overlap between gene lists from both tools: venn_
- Boxplot showing the differences in sizes between both tools: swarmplot_ - Boxplot showing the differences in sizes between both tools: swarmplot_
......
...@@ -2,8 +2,8 @@ ...@@ -2,8 +2,8 @@
#workdir: /home/bftan/CNA_results #directory to write output #workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2 #gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir: /home/beatrice/CNA_99_genegistic workdir: /exports/sasc/hmei/test_CNV #directory to write output
gisticdir: /home/beatrice/CNA_analysis/run_gistic2 gisticdir: /exports/sasc/hmei/GISTIC2 #directory to install GISTIC2
#Input details to download from firehose #Input details to download from firehose
cancer_type: SKCM cancer_type: SKCM
......
channels: channels:
- bioconda - bioconda
dependencies: dependencies:
- circos =0.69.6 - circos =0.69.2
...@@ -2,9 +2,13 @@ channels: ...@@ -2,9 +2,13 @@ channels:
- conda-forge - conda-forge
- edurand - edurand
- bioconda - bioconda
- pypi
dependencies: dependencies:
- python =3.6
- python-drmaa
- snakemake =4.5.0 - snakemake =4.5.0
- matplotlib-venn =0.11.5 - matplotlib-venn =0.11.5
- matplotlib =2.1.0
- pyensembl =1.1.0 - pyensembl =1.1.0
- seaborn =0.8.1 - seaborn =0.8.1
- pillow =5.0.0 - pillow =5.0.0
...@@ -11,6 +11,8 @@ rule do_GO_analysis: ...@@ -11,6 +11,8 @@ rule do_GO_analysis:
gene_ID_to_GO=os.path.join(workflow.basedir, config["ID_to_GO"]) if config["ID_to_GO"].startswith("input_files") else config["ID_to_GO"] gene_ID_to_GO=os.path.join(workflow.basedir, config["ID_to_GO"]) if config["ID_to_GO"].startswith("input_files") else config["ID_to_GO"]
benchmark: benchmark:
"Benchmarks/topGO." + str(datetime.datetime.now()).replace(" ", "_") + ".txt" "Benchmarks/topGO." + str(datetime.datetime.now()).replace(" ", "_") + ".txt"
resources:
mem_mb=50000
wrapper: wrapper:
"file:" + workflow.basedir + "/wrappers/topgo" "file:" + workflow.basedir + "/wrappers/topgo"
......
...@@ -2,12 +2,12 @@ ...@@ -2,12 +2,12 @@
#$ -S /bin/bash #$ -S /bin/bash
#$ -q all.q #$ -q all.q
#$ -N prioritization #$ -N prioritization
#$ -l h_vmem=20G #$ -l h_vmem=50G
#$ -cwd #$ -cwd
#$ -j Y #$ -j Y
#$ -V #$ -V
#$ -m be #$ -m be
#$ -M b.f.tan@lumc.nl #$ -M h.mei@lumc.nl
##Create or update conda environment and activate it ##Create or update conda environment and activate it
conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml && conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml &&
...@@ -18,8 +18,10 @@ snakemake -p \ ...@@ -18,8 +18,10 @@ snakemake -p \
--configfile config.yaml \ --configfile config.yaml \
--snakefile Snakefile \ --snakefile Snakefile \
--latency-wait 90 \ --latency-wait 90 \
--jobs 1 \ --jobs 10 \
--drmaa " -N preprocessor -q all.q -cwd -V" \
--drmaa-log-dir $(pwd)/.cluster_logs \
--max-jobs-per-second 10 \ --max-jobs-per-second 10 \
--restart-times 3 --restart-times 3 \
# --use-conda \ --use-conda \
# --conda-prefix ~/.conda --conda-prefix /exports/sasc/hmei/miniconda2/
...@@ -2,6 +2,7 @@ channels: ...@@ -2,6 +2,7 @@ channels:
- bioconda - bioconda
#- anaconda #- anaconda
dependencies: dependencies:
- r-base =3.4.1
- bioconductor-topgo =2.30.0 - bioconductor-topgo =2.30.0
- bioconductor-biomart =2.32.1 #2.34.1 needed due to error, not 2.34.0 - bioconductor-biomart =2.32.1 #2.34.1 needed due to error, not 2.34.0
- bioconductor-rgraphviz =2.22.0 - bioconductor-rgraphviz =2.22.0
......
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