Temporary work-around to test a new smgu

cbg-ethz · May 27, 2024 · 0dda12e · 0dda12e
1 parent fc9d717
commit 0dda12e
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diff --git a/tests/regression_tests.sh b/tests/regression_tests.sh
@@ -99,6 +99,7 @@ CONFIG_TRIM
        cat "${data_root}/config-extra.yaml"
        echo
     fi
+    export GIT_CLONE_PROTECTION_ACTIVE=false
 
     echo "config files ${config_file[*]}"
     PYTHONUNBUFFERED=1 snakemake \

diff --git a/workflow/envs/smallgenomeutilities.yaml b/workflow/envs/smallgenomeutilities.yaml
@@ -2,4 +2,20 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - smallgenomeutilities=0.4.0
+  - python >=3
+  - progress
+  - numpy
+  - pandas
+  - pyyaml
+  - biopython
+  - bcbio-gff
+  - pysam
+  - pysamstats
+  - scikit-learn
+  - scipy
+  - matplotlib-base
+  - mafft
+  - pip
+  - cython
+  - pip:
+    - git+https://github.com/cbg-ethz/smallgenomeutilities.git@dev#egg=smallgenomeutilities