Merge pull request #801 from maxplanck-ie/dev_adRn

Switched createEnvs to mamba

bin/snakePipes

@@ -287,7 +287,7 @@ def createCondaEnvs(args):
         h = md5hash.hexdigest()
 
         sys.stderr.write("Creating environment from {} in {}\n".format(os.path.join(baseDir, "shared/rules", env), condaDirUse))
-        cmd = ["conda", "env", "create", "--force", "--file", os.path.join(baseDir, "shared/rules", env)]
+        cmd = ["mamba", "env", "create", "--force", "--file", os.path.join(baseDir, "shared/rules", env)]
         if '--conda-prefix' in cf['snakemakeOptions'] and (args.condaDir or args.keepCondaDir):
             cmd += ["--prefix", os.path.join(condaDirUse, h)]
         else:

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.5.2
+  version: 2.5.3
 
 source:
   path: ../
@@ -14,12 +14,13 @@ requirements:
     - python >=3
   run:
     - python >=3.7.0
-    - snakemake ==5.18.0
+    - snakemake >=6.2.1
     - pandas
     - graphviz
     - fuzzywuzzy
     - pyyaml >=5.1
     - coreutils
+    - mamba
 
 test:
   commands:

docs/content/News.rst

@@ -1,14 +1,21 @@
 snakePipes News
 ===============
 
+
+snakePipes 2.5.3
+----------------
+
+* Switched to mamba by default at ``createEnvs`` function.
+
+
 snakePipes 2.5.2
 ----------------
 
 * snakemake version >= 6.2.1
 * python version >= 3.7
 * added snakeMake in readme
 * bug fix 777, 781
-* multiqc version = 1.10.1 to be able to report qc fir hic pipeline
+* multiqc version = 1.10.1 to be able to report QC for HiC pipeline
 * added snakemake catalog yaml
 
 

snakePipes/__init__.py

@@ -1 +1 @@
-__version__ = '2.5.2'
+__version__ = '2.5.3'