swap simuG to conda install

Author: pdimens

harpy/_conda.py

@@ -63,6 +63,7 @@ def create_conda_recipes():
             "bioconda::perl-math-random",
             "bioconda::perl-inline-c",
             "bioconda::perl-parse-recdescent",
+            "bioconda::simug",
             "conda-forge::numpy",
             "conda-forge::perl"
         ],

harpy/simulate.py

@@ -295,7 +295,6 @@ def snpindel(genome, snp_vcf, indel_vcf, only_vcf, output_dir, prefix, snp_count
         start_text.add_row("Heterozygosity:", f"{heterozygosity}")            
 
     fetch_rule(workflowdir, "simulate_snpindel.smk")
-    fetch_script(workflowdir, "simuG.pl")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "simulate_snpindel")
     configs = {
@@ -407,7 +406,6 @@ def inversion(genome, vcf, only_vcf, prefix, output_dir, count, min_size, max_si
         start_text.add_row("Heterozygosity:", f"{heterozygosity}")            
 
     fetch_rule(workflowdir, "simulate_variants.smk")
-    fetch_script(workflowdir, "simuG.pl")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "simulate_inversion")
     configs = {
@@ -522,7 +520,6 @@ def cnv(genome, output_dir, vcf, only_vcf, prefix, count, min_size, max_size, du
         start_text.add_row("Heterozygosity:", f"{heterozygosity}")            
 
     fetch_rule(workflowdir, "simulate_variants.smk")
-    fetch_script(workflowdir, "simuG.pl")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "simulate_cnv")
     configs = {
@@ -627,7 +624,6 @@ def translocation(genome, output_dir, prefix, vcf, only_vcf, count, centromeres,
         start_text.add_row("Heterozygosity:", f"{heterozygosity}")            
 
     fetch_rule(workflowdir, "simulate_variants.smk")
-    fetch_script(workflowdir, "simuG.pl")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "simulate_translocation")
     configs = {

harpy/snakefiles/simulate_snpindel.smk

@@ -148,13 +148,13 @@ rule simulate_diploid:
         f"{outdir}/logs/{outprefix}.hap{{haplotype}}.log"
     params:
         prefix = f"{outdir}/diploid/{outprefix}.hap{{haplotype}}",
-        simuG = f"{outdir}/workflow/scripts/simuG.pl",
+        #simuG = f"{outdir}/workflow/scripts/simuG.pl",
         snp = f"-snp_vcf {outdir}/diploid/{outprefix}.snp.hap{{haplotype}}.vcf" if snp else "",
         indel = f"-indel_vcf {outdir}/diploid/{outprefix}.indel.hap{{haplotype}}.vcf" if indel else ""
     conda:
         f"{envdir}/simulations.yaml"
     shell:
-        "perl {params.simuG} -refseq {input.geno} -prefix {params.prefix} {params.snp} {params.indel} > {log}"
+        "simuG -refseq {input.geno} -prefix {params.prefix} {params.snp} {params.indel} > {log}"
 
 rule workflow_summary:
     default_target: True

harpy/snakefiles/simulate_variants.smk

@@ -62,12 +62,12 @@ rule simulate_haploid:
         f"{outdir}/logs/{outprefix}.log"
     params:
         prefix = f"{outdir}/{outprefix}",
-        simuG = f"{outdir}/workflow/scripts/simuG.pl",
+        #simuG = f"{outdir}/workflow/scripts/simuG.pl",
         parameters = variant_params
     conda:
         f"{envdir}/simulations.yaml"
     shell:
-        "perl {params.simuG} -refseq {input.geno} -prefix {params.prefix} {params.parameters} > {log}"
+        "simuG -refseq {input.geno} -prefix {params.prefix} {params.parameters} > {log}"
 
 rule diploid_variants:
     input: