try to cache image

.github/workflows/tests.yml

@@ -72,6 +72,16 @@ jobs:
           python3 -m pip install --upgrade build && python3 -m build
           pip install dist/*.whl
           resources/buildforCI.sh
+      - name: Clear space
+        run: rm -rf /opt/hostedtoolcache
+      - name: pull image
+        shell: micromamba-shell {0}
+        run: snakemake -s resources/container/pullcontainerCI.smk --sdm conda apptainer -q
+      - name: upload singularity
+        uses: actions/upload-artifact@v4
+        with:
+          name: deps-image
+          path: .snakemake/singularity
 
   dmux_gen1:
     needs: [changes, pkgbuild]
@@ -99,6 +109,10 @@ jobs:
           resources/buildforCI.sh
       - name: Clear space
         run: rm -rf /opt/hostedtoolcache
+      - name: Download a single artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: deps-image
       - name: harpy demultiplex
         shell: micromamba-shell {0}
         run: harpy demultiplex gen1  --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*

resources/container/pullcontainerCI.smk

@@ -0,0 +1,63 @@
+containerized: "docker://pdimens/harpy:latest"
+
+import os
+import shutil
+
+condachannels = ["bioconda","conda-forge","defaults"]
+environ = {
+    "qc" : ["bioconda::falco", "bioconda::fastp", "bioconda::multiqc", "bioconda::pysam=0.22"],
+    "align": ["bioconda::bwa", "bioconda::ema","conda-forge::icu","conda-forge::libzlib", "bioconda::minimap2", "bioconda::samtools=1.20", "bioconda::seqtk", "bioconda::tabix", "conda-forge::xz"],
+    "snp": ["bioconda::bcftools=1.20", "bioconda::freebayes=1.3.6"],
+    "sv": ["bioconda::leviathan", "bioconda::naibr-plus"],
+    "phase" : ["bioconda::hapcut2", "bioconda::whatshap"],
+    "simulations" : ["conda-forge::perl", "bioconda::perl-math-random", "bioconda::perl-inline-c", "bioconda::perl-parse-recdescent", "conda-forge::numpy", "bioconda::dwgsim", "alienzj::msort"],
+    "r" : ["conda-forge::r-xml2", "bioconda::bioconductor-complexheatmap", "conda-forge::r-highcharter", "conda-forge::r-circlize", "r::r-biocircos", "conda-forge::r-dt", "conda-forge::r-flexdashboard", "conda-forge::r-ggplot2", "conda-forge::r-ggridges", "conda-forge::r-plotly", "conda-forge::r-tidyr", "bioconda::r-stitch"]
+}
+os.makedirs(os.getcwd() + ".harpy_envs", exist_ok = True)
+for i in environ:
+    # overwrites existing
+    with open(os.getcwd() + f"/.harpy_envs/{i}.yaml", "w") as yml:
+        yml.write(f"name: {i}\n")
+        yml.write("channels:\n  - ")
+        yml.write("\n  - ".join(condachannels))
+        yml.write("\ndependencies:\n  - ")
+        yml.write("\n  - ".join(environ[i]) + "\n")
+
+rule all:
+    input:
+        collect("{conda}.env", conda = ["qc","align","snp","sv","phase","r","simulations"])
+
+rule qc:
+    output: "qc.env"
+    conda: os.getcwd() + "/.harpy_envs/qc.yaml"
+    shell: "touch {output}"
+
+rule align:
+    output: "align.env"
+    conda: os.getcwd() + "/.harpy_envs/align.yaml"
+    shell: "touch {output}"
+
+rule snp:
+    output: "snp.env"
+    conda: os.getcwd() + "/.harpy_envs/snp.yaml"
+    shell: "touch {output}"
+
+rule sv:
+    output: "sv.env"
+    conda: os.getcwd() + "/.harpy_envs/sv.yaml"
+    shell: "touch {output}"
+
+rule phase:
+    output: "phase.env"
+    conda: os.getcwd() + "/.harpy_envs/phase.yaml"
+    shell: "touch {output}"
+
+rule r_env:
+    output: "r.env"
+    conda: os.getcwd() + "/.harpy_envs/r.yaml"
+    shell: "touch {output}"
+
+rule simulations:
+    output: "simulations.env"
+    conda: os.getcwd() + "/.harpy_envs/simulations.yaml"
+    shell: "touch {output}"