From 0dda12ee7b49d684e8cd3fba587b92ca68d263ff Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Mon, 27 May 2024 22:56:08 +0200
Subject: [PATCH] Temporary work-around to test a new smgu

---
 tests/regression_tests.sh               |  1 +
 workflow/envs/smallgenomeutilities.yaml | 18 +++++++++++++++++-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/tests/regression_tests.sh b/tests/regression_tests.sh
index 35d2a040..b180a81a 100755
--- 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
index 6df73ff5..8d7fb593 100644
--- 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