Fix #346

metagenome-atlas · Dec 21, 2020 · 6d80e07 · 6d80e07
1 parent 9702700
commit 6d80e07
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/atlas/default_values.py b/atlas/default_values.py
@@ -217,6 +217,7 @@ def make_default_config():
                            }
 
     conf['eggNOG_use_virtual_disk']= False
+    conf['virtual_disk'] = "/dev/shm"
 
     # binning
     conf["perform_genome_binning"] = True

diff --git a/atlas/rules/genecatalog.snakefile b/atlas/rules/genecatalog.snakefile
@@ -459,10 +459,9 @@ rule eggNOG_annotation:
     output:
         temp("{folder}/{prefix}.emapper.annotations")
     params:
-        data_dir = "/dev/shm" if config['eggNOG_use_virtual_disk'] else EGGNOG_DIR,
+        data_dir = config['virtual_disk'] if config['eggNOG_use_virtual_disk'] else EGGNOG_DIR,
         prefix = "{folder}/{prefix}",
         copyto_shm="t" if config['eggNOG_use_virtual_disk'] else 'f'
-
     threads:
         config.get("threads", 1)
     resources:
@@ -478,7 +477,7 @@ rule eggNOG_annotation:
 
             if [ {params.copyto_shm} == "t" ] ;
             then
-                cp {params.data_dir}/eggnog.db /dev/shm/eggnog.db 2> {log}
+                cp {EGGNOG_DIR}/eggnog.db {params.data_dir}/eggnog.db 2> {log}
             fi
 
             emapper.py --annotate_hits_table {input.seed} --no_file_comments \