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
metagenome-atlas · Jul 23, 2020 · 76fd72a · 76fd72a
1 parent 65a018c
commit 76fd72a
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/.circleci/config.yml b/.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:

diff --git a/atlas/__init__.py b/atlas/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "2.3.5"
+__version__ = "2.4.0"
 
 from .scripts import utils
 

diff --git a/atlas/envs/gtdbtk.yaml b/atlas/envs/gtdbtk.yaml
@@ -3,4 +3,4 @@ channels:
 - bioconda
 - defaults
 dependencies:
-- gtdbtk =1.0.*
+- gtdbtk =1.3.*
diff --git a/atlas/rules/download.snakefile b/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