Aborted attempt to fix CI

Squashed commit of the following: commit 46573fd Author: Kevin Murray <[email protected]> Date: Fri May 6 16:50:53 2022 +0200 df commit 82081c7 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:45:22 2022 +0200 fixup! fixup! fixup! fixup! fixup! tryfix: ci commit cc6a462 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:42:59 2022 +0200 fixup! fixup! fixup! fixup! tryfix: ci commit 555aa1c Author: Kevin Murray <[email protected]> Date: Fri May 6 16:40:00 2022 +0200 fixup! fixup! fixup! tryfix: ci commit 1210322 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:31:50 2022 +0200 fixup! fixup! tryfix: ci commit 33aedf2 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:29:14 2022 +0200 fixup! tryfix: ci commit 7f0de19 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:27:53 2022 +0200 tryfix: ci commit f5e41d9 Author: Kevin Murray <[email protected]> Date: Fri May 6 16:25:31 2022 +0200 tryfix: ci
kdm9 · May 6, 2022 · 62ec141 · 62ec141
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commit 62ec141
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Showing 3 changed files with 15 additions and 12 deletions.
diff --git a/.github/workflows/run-snakemake.yml b/.github/workflows/run-snakemake.yml
@@ -13,16 +13,17 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: setup-conda
-        uses: s-weigand/setup-[email protected]
+      - name: setup-mamba
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-conda: true
-          update-conda: true
-          conda-channels: "defaults,conda-forge,bioconda,kdm801"
+          mamba-version: "*"
+          channels: bioconda,kdm801,conda-forge,defaults
+          channel-priority: true
 
       - name: setup and run Snakemake
+        shell: bash -el {0}
         run: |
-          conda install mamba pip
+          mamba info
           pushd example
           source setup.sh
           snakemake --snakefile Snakefile -j 4 --use-conda --conda-frontend mamba

diff --git a/example/environment.yml → example/environment_demo.yml b/example/environment.yml → example/environment_demo.yml
@@ -7,7 +7,9 @@ channels:
 dependencies:
   - python
   - snakemake
-  - acanthophis
   - ncdu
-  - git-annex
-  - pynvim
+  - pip
+  - numpy
+  - msprime
+  - wgsim
+  - samtools
diff --git a/example/setup.sh b/example/setup.sh
@@ -1,13 +1,13 @@
 #!/bin/bash
 #set -xeuo pipefail
-mamba env update -f environment.yml
-mamba activate acanthophis-demo
+mamba env update -f environment_demo.yml
+conda activate acanthophis-demo
 pip install -e ../
 acanthophis-init --yes
 # download kraken DB
 mkdir -p data/dbs/kraken/viral
 pushd  data/dbs/kraken/viral
-test -f  k2_viral_20201202.tar.gz || wget https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20201202.tar.gz
+test -f  k2_viral_20201202.tar.gz || wget -q https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20201202.tar.gz
 tar xvf k2_viral_20201202.tar.gz
 popd
 snakemake --snakefile Snakefile.generate-rawdata -j 4 --use-conda --conda-frontend mamba