diff --git a/atlas/default_values.py b/atlas/default_values.py index 96f65a5a..6388ccf1 100644 --- 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 index 2d028945..3b8266a2 100644 --- 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 \