Fixed component_version comparison in datadump.py

bifrost_chewbbaca/datadump.py

@@ -86,10 +86,15 @@ def datadump(samplecomponent_ref_json: Dict):
 
 
 def extract_digits_from_component_version(component_str):
-    version_re = re.compile(".*__(v.*)__.*")
+    version_re = re.compile(r".*__v(\d+\.\d+\.\d+)(__)?.*")
     version_group = re.match(version_re, component_str).groups()[0]
-    version_digits = int("".join([i for i in version_group if i.isdigit()]))
+    version_digits = tuple([int(i) for i in version_group.split(".") if i.isdigit()])
     return version_digits
+# def extract_digits_from_component_version(component_str):
+#     version_re = re.compile(".*__(v.*?)(__)?.*$")
+#     version_group = re.match(version_re, component_str).groups()[0]
+#     version_digits = int("".join([i for i in version_group if i.isdigit()]))
+#     return version_digits
 
 
 datadump(

environment.yml

@@ -3,12 +3,14 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - snakemake-minimal>=5.31.1 # updated from 5.7.1 because of envvars
-  - blast>=2.14.0 # updated from blast>=2.9
-  - prodigal>=2.6.3
-  - chewbbaca>=3.2.0
+  - snakemake-minimal==5.7.1
+  - blast=2.9
+  - prodigal=2.6.3
+  - chewbbaca=3.2.0
   - pip
   - pip:
+    - jsonschema<4
+    - warlock==1.3.3
     - pytest
     - pytest-cov
     - pytest-profiling
@@ -17,5 +19,3 @@ dependencies:
     - argh
     - watchdog
     - bifrostlib
-    - black
-    - -e .

install.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -euo pipefail
+
 helpFunction()
 {
    echo ""
@@ -39,7 +41,7 @@ if [ "$parameterI" == "COMP" ]
 then
   echo "Starting computerome install"
   module load tools computerome_utils/2.0
-  module load tools anaconda3/2022.10
+  module load tools $CONDA_VERSION
   #if $BIFROST_CONDA_PATH is not set then exit with help message
   if [ -z "$BIFROST_CONDA_PATH" ]
   then
@@ -121,7 +123,7 @@ if test -f "$REQ_TXT";
 then
   echo "Making conda env"
   echo "$ENV_NAME will be created"
-  conda env create -f "$REQ_TXT" --name $ENV_NAME
+  mamba env create --file "$REQ_TXT" --name $ENV_NAME
 else
   echo "environment.yml file cannot be found in the script folder"
   exit 1
@@ -148,7 +150,5 @@ fi
 if test -f "$CUSTOM_INSTALL_PATH";
 then
   echo -e "\nRunning custom_install.sh"
-  eval "$(conda shell.bash hook)"
-  conda activate $ENV_NAME
-  bash $CUSTOM_INSTALL_PATH -i $parameterI
-fi
+  bash -i $CUSTOM_INSTALL_PATH $ENV_NAME #-i required for interactive mode to active env
+fi