conda added

Author: Emrah Akkoyun

workflow/rules/ml_tree.smk

@@ -5,6 +5,8 @@ rule ml_tree:
         bestTree = "{workdir}/results/{query_fasta}/3_mltree/{query_fasta}.raxml.bestTree",
     params:
         raxml_out_name = "{query_fasta}",
+    conda:
+        "../envs/raxml-ng.yml"
     benchmark:
         "{workdir}/workflow/logs/benchmarks/{query_fasta}_ml_tree.out"
     cache: True

workflow/scripts/raxml-ng.sh

@@ -7,8 +7,6 @@ raxml_seed=$4
 output_tree=$5
 tree_num=$6
 
-module load raxml-ng-0.9.0
-
 # recommended # threads
 thread_num=`raxml-ng --parse --msa $trimmed_msa --model $raxml_model --nofile|grep "Recommended number of threads"|awk -F: {'print $2'}| xargs`
 echo "Recommended number of thread: $thread_num"