From 4bbb6295a555e24e435295b762f6f5a2426d9234 Mon Sep 17 00:00:00 2001
From: alienzj <alienchuj@gmail.com>
Date: Tue, 30 Jun 2020 09:16:10 +0800
Subject: [PATCH] update envs, update to v0.9.1

---
 metapi/__about__.py                         | 2 +-
 metapi/config.yaml                          | 3 ++-
 metapi/corer.py                             | 8 ++++++--
 metapi/envs/bioenv2.yaml                    | 1 -
 metapi/envs/bioenv3.6.yaml                  | 6 ++++++
 metapi/envs/{bioenv.yaml => bioenv3.7.yaml} | 2 +-
 metapi/rules/dereplicate.smk                | 2 ++
 7 files changed, 18 insertions(+), 6 deletions(-)
 create mode 100644 metapi/envs/bioenv3.6.yaml
 rename metapi/envs/{bioenv.yaml => bioenv3.7.yaml} (96%)

diff --git a/metapi/__about__.py b/metapi/__about__.py
index c0fd53d1..1a8d5f8c 100644
--- a/metapi/__about__.py
+++ b/metapi/__about__.py
@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 
-__version__ = '0.9.0'
+__version__ = '0.9.1'
 __author__ = "Jie Zhu"
diff --git a/metapi/config.yaml b/metapi/config.yaml
index a0e86b62..5f26ea68 100644
--- a/metapi/config.yaml
+++ b/metapi/config.yaml
@@ -358,5 +358,6 @@ upload:
     reference_genome: ""
 
 envs:
-  bioenv: "envs/bioenv.yaml"
+  bioenv3.7: "envs/bioenv3.7.yaml"
+  bioenv3.6: "envs/bioenv3.6.yaml"
   bioenv2: "envs/bioenv2.yaml"
diff --git a/metapi/corer.py b/metapi/corer.py
index bdc28d23..23a9a792 100755
--- a/metapi/corer.py
+++ b/metapi/corer.py
@@ -91,8 +91,12 @@ def init(args):
         print(project.__str__())
         project.create_dirs()
         conf, cluster = project.get_config()
-        conf["envs"]["bioenv"] = os.path.join(
-            os.path.realpath(args.workdir), "envs/bioenv.yaml"
+
+        conf["envs"]["bioenv3.7"] = os.path.join(
+            os.path.realpath(args.workdir), "envs/bioenv3.7.yaml"
+        )
+        conf["envs"]["bioenv3.6"] = os.path.join(
+            os.path.realpath(args.workdir), "envs/bioenv3.6.yaml"
         )
         conf["envs"]["bioenv2"] = os.path.join(
             os.path.realpath(args.workdir), "envs/bioenv2.yaml"
diff --git a/metapi/envs/bioenv2.yaml b/metapi/envs/bioenv2.yaml
index 1649a4cf..7f70bd85 100644
--- a/metapi/envs/bioenv2.yaml
+++ b/metapi/envs/bioenv2.yaml
@@ -3,6 +3,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  #- drep=2.6.2
   - humann2=2.8.1
   - metaphlan2=2.8
diff --git a/metapi/envs/bioenv3.6.yaml b/metapi/envs/bioenv3.6.yaml
new file mode 100644
index 00000000..e239061b
--- /dev/null
+++ b/metapi/envs/bioenv3.6.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - drep=2.6.2
diff --git a/metapi/envs/bioenv.yaml b/metapi/envs/bioenv3.7.yaml
similarity index 96%
rename from metapi/envs/bioenv.yaml
rename to metapi/envs/bioenv3.7.yaml
index 5761cd4b..1b96bf49 100644
--- a/metapi/envs/bioenv.yaml
+++ b/metapi/envs/bioenv3.7.yaml
@@ -7,7 +7,7 @@ dependencies:
   - bowtie2>=2.3.5.1
   - bracken>=2.6.0
   - bwa>=0.7.17
-  #- checkm-genome>=1.1.2
+  - checkm-genome>=1.1.2
   - concoct>=1.1.0
   - das_tool>=1.1.2
   - diamond>=0.9.32
diff --git a/metapi/rules/dereplicate.smk b/metapi/rules/dereplicate.smk
index 3efe85b0..7df0c67c 100644
--- a/metapi/rules/dereplicate.smk
+++ b/metapi/rules/dereplicate.smk
@@ -56,6 +56,8 @@ if config["params"]["dereplicate"]["drep"]["do"]:
         log:
             os.path.join(config["output"]["dereplicate"],
                          "logs/hmq.bins.{assembler}.{binner}.drep.log")
+        conda:
+            config["envs"]["bioenv3.6"]
         params:
             bin_suffix = "fa",
             filtering_genome_min_length = \