Split conda environments to prevent solving issues

environments/tobias.yaml

@@ -3,25 +3,34 @@ name: TOBIAS_ENV
 channels:
   - bioconda
   - conda-forge
+  - defaults
 
 dependencies:
-  - python=3
-  - snakemake>=5.4
-  - uropa=3
-  - samtools
-  - moods
-  - unzip
-  - r-devtools
-  - r-knitr
-  - r-lme4
-  - r-htmltable
-  - tobias>=0.9
-  - r-hmisc
-  - r-pbkrtest
-  - r-openxlsx
-  - r-rio
-  - r-car
-  - bioconductor-deseq2
-  - intervene
-  - igvtools
-  - icu
+  - python=3.6.7
+  - bioconda::snakemake>=5.4
+  - unzip=6.0
+  - igvtools=2.5.3
+  - openssl=1.0.2
+  - pysam=0.15.3
+  - gimmemotifs=0.13.1
+  - samtools=1.5
+  - sklearn-contrib-lightning=0.5.0
+  - scikit-learn=0.22.1
+  - scipy=1.2.1
+  - icu=64.2
+  - ncurses=6.1
+  - numpy=1.17.5
+  - boto3=1.11.9
+  - setuptools=45.1.0
+  - botocore=1.14.9
+  - pandas=0.25.3
+  - pip=20.0.2
+  - libpng=1.6.37
+  - pip:
+    - adjusttext==0.7.3
+    - moods-python==1.9.4.1
+    - pybigwig==0.3.17
+    - tobias>=0.9
+    - pypdf2==1.26.0
+    - wand==0.5.8
+    - xgboost==0.90

environments/tools.yaml

@@ -0,0 +1,4 @@
+name: tools_env
+
+dependencies:
+  - intervene

environments/uropa.yaml

@@ -0,0 +1,7 @@
+name: uropa_env
+
+channels:
+  - bioconda
+
+dependencies:
+  - uropa

environments/wilson.yaml

@@ -0,0 +1,29 @@
+name: wilson_env
+
+dependencies:
+  - r-devtools
+  - r-data.table==1.12.8 
+  - r-plotly
+  - r-shiny
+  - r-shinydashboard
+  - r-shinythemes
+  - r-htmltools
+  - bioconductor-deseq2
+  - r-ggrepel
+  - r-biocmanager
+  - r-colourpicker
+  - bioconductor-iranges
+  - bioconductor-genefilter
+  - r-markdown
+  - r-viridis
+  - r-tidyr
+  - r-reshape
+  - r-log4r
+  - r-shape
+  - r-ggpubr
+  - r-catools
+  - r-factominer
+  - r-heatmaply==1.0.0
+  - r-car
+  - r-rjson
+  - r-circlize==0.4.8

snakefiles/preprocessing.snake

@@ -25,7 +25,8 @@ rule copy_flatfiles:
 rule write_config:
 	output:
 		os.path.join(OUTPUTDIR, "config.yaml")
-	priority: 100
+	priority: 
+		100
 	run:
 		import yaml
 		with open(output[0], 'w') as yaml_file:
@@ -43,8 +44,10 @@ rule conditionbam:
 	output:
 		bam = os.path.join(OUTPUTDIR, "mapping", "{condition}.bam"),
 		bai = os.path.join(OUTPUTDIR, "mapping", "{condition}.bam.bai")
-	threads: 99
-	message: "Joining individual bamfiles from condition {wildcards.condition}"
+	threads: 
+		99
+	message: 
+		"Joining individual bamfiles from condition {wildcards.condition}"
 	run:
 		if len(input) > 1:
 			shell("samtools merge -@ {threads} {output.bam} {input}")
@@ -69,9 +72,12 @@ rule macs:
 	output: 
 		macs = os.path.join(OUTPUTDIR, "peak_calling", "{condition}", "{sample_id}_peaks.broadPeak"),
 		raw = os.path.join(OUTPUTDIR, "peak_calling", "{condition}", "{sample_id}_raw.bed")
-	log: os.path.join(OUTPUTDIR, "logs", "{condition}_{sample_id}_peak_calling.log")
-	message: "Running macs2 with .bam-file: {input}"
-	conda: os.path.join(environments_dir, "macs.yaml")
+	log: 
+		os.path.join(OUTPUTDIR, "logs", "{condition}_{sample_id}_peak_calling.log")
+	message: 
+		"Running macs2 with .bam-file: {input}"
+	conda: 
+		os.path.join(environments_dir, "macs.yaml")
 	params:
 		"--name {sample_id}",
 		"--outdir " + os.path.join(OUTPUTDIR, "peak_calling", "{condition}"),
@@ -107,7 +113,8 @@ rule merge_condition_peaks:
 		[os.path.join(OUTPUTDIR, "peak_calling", condition + "_union.bed") for condition in CONDITION_IDS]
 	output: 
 		temp(os.path.join(OUTPUTDIR, "peak_calling", "all_merged.tmp"))
-	message: "Merging peaks across conditions"
+	message: 
+		"Merging peaks across conditions"
 	shell:
 		"cat {input} | sort -k1,1 -k2,2n | bedtools merge -d 5 -c 4 -o distinct > {output}"
 
@@ -170,10 +177,14 @@ rule uropa:
 		finalhits_sub = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated_finalhits_sub.txt"),
 		peaks = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated.bed"),
 		header = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated_header.txt"),
-	threads: 99
-	log: os.path.join(OUTPUTDIR, "logs", "uropa.log")
+	threads: 
+		99
+	log: 
+		os.path.join(OUTPUTDIR, "logs", "uropa.log")
 	params:
 		prefix = os.path.join(OUTPUTDIR, "peak_annotation", "all_merged_annotated")
+	conda: 
+		os.path.join(environments_dir, "uropa.yaml")
 	shell:
 		"uropa --input {input.config} --prefix {params.prefix} --threads {threads} --log {log}; "
 		"cut -f 1-4,7-13,16-19 {output.finalhits} > {output.finalhits_sub}; " #Get a subset of columns

snakefiles/visualization.snake

@@ -48,6 +48,8 @@ rule plot_venn:
 		"--output " + os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots"),
 		"--names " + ",".join(["'{0} bound sites'".format(condition) for condition in CONDITION_IDS]),
 		"--title " + "'Overlap of sites for TF: {TF}'"
+	conda:
+		"../environments/tools.yaml"
 	shell: 
 		"intervene venn --input {input} {params} > /dev/null ; "
 		"cp {output.raw} {output.final}"
@@ -105,7 +107,8 @@ rule join_pdfs:
 		lambda wildcards: expand(os.path.join(OUTPUTDIR, "TFBS", "{TF}", "plots", "{TF}_{{plotname}}.pdf"), TF=get_TF_ids(wildcards))
 	output:
 		os.path.join(OUTPUTDIR, "overview", "all_{plotname}.pdf")
-	message: "Joining {wildcards.plotname} plots from all TFs"
+	message: 
+		"Joining {wildcards.plotname} plots from all TFs"
 	shell:
 		"TOBIAS MergePDF --input {input} --output {output} >/dev/null"
 

snakefiles/wilson.snake

@@ -14,6 +14,8 @@ rule wilson_app:
 	params:
 		wilsondir = os.path.join(OUTPUTDIR, "wilson"),
 		scripts = scripts_dir
+	conda:
+		"../environments/wilson.yaml"
 	shell:
 		"mkdir -p {params.wilsondir}; "
 		"unzip -o {input} -d {params.wilsondir}; "
@@ -39,6 +41,8 @@ rule convert_individual_overview:
 		app = os.path.join(OUTPUTDIR, "wilson", "app.R")
 	params:
 		scripts = scripts_dir
+	conda:
+		"../environments/wilson.yaml"
 	output:
 		os.path.join(OUTPUTDIR, "wilson", "data", "{TF}_overview.clarion")
 	shell:
@@ -55,6 +59,8 @@ rule convert_global_overview:
 	params: 
 		overview = os.path.join(OUTPUTDIR, "overview", "*_results.txt"),
 		scripts = scripts_dir
+	conda:
+		"../environments/wilson.yaml"
 	shell:
 		"Rscript {params.scripts}/convert_data.R --input {params.overview} --output {output} --condition_names {input.condition_names} &> /dev/null "