new changes for conda recipe

TurakhiaLab · Aug 2, 2024 · 04422bb · 04422bb
1 parent 954f9b3
commit 04422bb
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Showing 3 changed files with 4 additions and 5 deletions.
diff --git a/roadies_env.sh b/roadies_env.sh
@@ -18,7 +18,7 @@ fi
 source "${CONDA_PATH}/etc/profile.d/conda.sh"  # Temporarily source conda for this script
 source "${CONDA_PATH}/etc/profile.d/mamba.sh"  # Temporarily source mamba for this script
 if ! conda env list | grep -q "roadies_env"; then
-    mamba create -y -c conda-forge -c bioconda --name roadies_env snakemake alive-progress biopython iqtree=2.2.0.3 numpy lastz mashtree matplotlib seaborn treeswift=1.1.28 fasttree=2.1.11 python=3.11 raxml-ng ete3
+    mamba create -y -c conda-forge -c bioconda --name roadies_env snakemake alive-progress biopython iqtree=2.2.0.3 numpy lastz mashtree matplotlib seaborn treeswift=1.1.28 fasttree=2.1.11 python=3.9 raxml-ng ete3
 fi
 conda activate roadies_env
 
@@ -27,7 +27,6 @@ if [ ! -d "ASTER-Linux" ]; then
     wget -q https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip -O Linux.zip
     unzip -q Linux.zip
     cd ASTER-Linux
-    make
     g++ -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro2
     cd ..
 fi

diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -91,7 +91,7 @@ rule pasta:
 			if [ "$all_matched" = true ]; then
 				cp "$input_file" "$output_file"
 			else
-				python pasta/run_pasta.py -i {input} -j {params.prefix} --alignment-suffix={params.suffix} --num-cpus {threads}
+				run_pasta.py -i {input} -j {params.prefix} --alignment-suffix={params.suffix} --num-cpus {threads}
 			fi
 		fi
 		touch {output}
@@ -110,7 +110,7 @@ rule filtermsa:
 		"../envs/filtermsa.yaml"
 	shell:
 		'''
-		python pasta/run_seqtools.py -masksitesp {params.n} -filterfragmentsp {params.m} -infile {input} -outfile {output}
+		run_seqtools.py -masksitesp {params.n} -filterfragmentsp {params.m} -infile {input} -outfile {output}
 			
 		'''
 
diff --git a/workflow/rules/mashtree.smk b/workflow/rules/mashtree.smk
@@ -132,7 +132,7 @@ rule mashtree:
 		'''
 		if [[ `grep -n '>' {input} | wc -l` -gt {params.m} ]] || [[ `awk 'BEGIN{{l=0;n=0;st=0}}{{if (substr($0,1,1) == ">") {{st=1}} else {{st=2}}; if(st==1) {{n+=1}} else if(st==2) {{l+=length($0)}}}} END{{if (n>0) {{print int((l+n-1)/n)}} else {{print 0}} }}' {input}` -gt {params.max_len} ]]
 		then
-			mashtree --mindepth 0 --numcpus {threads} --kmerlength 10 {params.gene_dir}/*.fa > {output}
+			mashtree.pl --mindepth 0 --numcpus {threads} --kmerlength 10 {params.gene_dir}/*.fa > {output}
 		fi
 		touch {output}
 		'''