updae to new GTDB (#306)

* updae to new GTDB

fix #404

* new version specific download path

* update verion 2.4

* define mem 4 via --config in ciricle ci test assembly

Author: SilasK

.circleci/config.yml

@@ -136,7 +136,7 @@ jobs:
           name: test assembly
           command: |
               source activate ./atlasenv
-              .test/test_assembly.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 --omit-from build_qc_report build_assembly_report
+              .test/test_assembly.sh --resources mem=$MEM java_mem=$MEM --config  threads=$N_THREADS mem=$MEM --jobs=$N_THREADS --restart-times=2 --omit-from build_qc_report build_assembly_report
       # - store_test_results:
       #     path: .test/Test_assembly/reports
       # - store_artifacts:

atlas/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.3.5"
+__version__ = "2.4.0"
 
 from .scripts import utils
 

atlas/envs/gtdbtk.yaml

@@ -3,4 +3,4 @@ channels:
 - bioconda
 - defaults
 dependencies:
-- gtdbtk =1.0.*
+- gtdbtk =1.3.*

atlas/rules/download.snakefile

@@ -26,7 +26,7 @@ CHECKM_ARCHIVE = "checkm_data_v1.0.9.tar.gz"
 CAT_DIR= os.path.join(DBDIR,'CAT')
 CAT_flag_downloaded = os.path.join(CAT_DIR,'downloaded')
 EGGNOG_DIR = os.path.join(DBDIR,'EggNOGV2')
-GTDBTK_DATA_PATH=os.path.join(DBDIR,"GTDB-TK")
+GTDBTK_DATA_PATH=os.path.join(DBDIR,"GTDB_V05")
 CONDAENV = "../envs"
 
 # note: saving OG_fasta.tar.gz in order to not create secondary "success" file