Merge pull request #295 from metagenome-atlas/demo

fix snakemake to 5.9.1 because of ChildIOException

.circleci/config.yml

@@ -87,8 +87,7 @@ jobs:
           name: install environements
           command: |
               source activate ./atlasenv
-              alias conda=mamba
-              atlas run all -w .test/Getenvs --create-envs-only
+              atlas run all -w .test/Getenvs --create-envs-only --omit-from build_qc_report build_assembly_report build_bin_report
       - save_cache:
           key: conda-environements-{{ checksum "conda_envs.tar"  }}
           paths:
@@ -137,12 +136,12 @@ jobs:
           name: test assembly
           command: |
               source activate ./atlasenv
-              .test/test_assembly.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2
-      - store_test_results:
-          path: .test/Test_assembly/reports
-      - store_artifacts:
-          path: .test/Test_assembly/reports
-          destination: assembly_results
+              .test/test_assembly.sh --resources mem=$MEM java_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:
+      #     path: .test/Test_assembly/reports
+      #     destination: assembly_results
 
       - run:
           name: run genecatalog

atlas/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.3.0"
+__version__ = "2.3.2"
 
 from .scripts import utils
 

atlas/envs/report.yaml

@@ -6,8 +6,8 @@ dependencies:
     - numpy=1.13.1
     - python=3.6
     - pandas=0.20.3
-    - plotly=2.2.2
-    - ipython=6.2.1
+    - plotly
+    - ipython
     - seaborn=0.8
     - snakemake=5.7.4 #or5.8.2 sheetname error
     - docutils

atlasenv.yml

@@ -4,7 +4,7 @@ channels:
   - defaults
 dependencies:
   - python=3.6
-  - snakemake
+  - snakemake=5.9.1
   - pandas
   - bbmap=37.78
   - click=7