bump version

Author: thylakoid

Dockerfile

@@ -1,6 +1,6 @@
 FROM condaforge/mambaforge:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="22cb0e992026e0a51e7865cde3fe4f121ebee6884b03236720bb5eac7c59f150"
+LABEL io.github.snakemake.conda_env_hash="5f0db39474f146c3c24b91d80a56371ba87ea9f8c93b49e0b3e62cfa9a4e195b"
 
 # Step 1: Retrieve conda environments
 
@@ -142,6 +142,18 @@ COPY workflow/envs/eggnog.yaml /conda-envs/5ab146b4f8a224935ba7154dde2d9065/envi
 RUN mkdir -p /conda-envs/5bf95c616c0ba0db0478590fc40d2505
 COPY workflow/envs/fasttree.yaml /conda-envs/5bf95c616c0ba0db0478590fc40d2505/environment.yaml
 
+# Conda environment:
+#   source: workflow/envs/gapseq.yaml
+#   prefix: /conda-envs/f19f15c6c742ae3e49b0435d689406c1
+#   name: gapseq
+#   channels:
+#     - bioconda
+#     - conda-forge
+#   dependencies:
+#     - gapseq
+RUN mkdir -p /conda-envs/f19f15c6c742ae3e49b0435d689406c1
+COPY workflow/envs/gapseq.yaml /conda-envs/f19f15c6c742ae3e49b0435d689406c1/environment.yaml
+
 # Conda environment:
 #   source: workflow/envs/gtdbtk.yaml
 #   prefix: /conda-envs/df2a53a81d11717a831dda8590f53cd5
@@ -307,6 +319,7 @@ RUN mamba env create --prefix /conda-envs/b5c6b988e4a325065292b3d680193d32 --fil
     mamba env create --prefix /conda-envs/06095a97a5b2a1ad8552af1df6312c10 --file /conda-envs/06095a97a5b2a1ad8552af1df6312c10/environment.yaml && \
     mamba env create --prefix /conda-envs/5ab146b4f8a224935ba7154dde2d9065 --file /conda-envs/5ab146b4f8a224935ba7154dde2d9065/environment.yaml && \
     mamba env create --prefix /conda-envs/5bf95c616c0ba0db0478590fc40d2505 --file /conda-envs/5bf95c616c0ba0db0478590fc40d2505/environment.yaml && \
+    mamba env create --prefix /conda-envs/f19f15c6c742ae3e49b0435d689406c1 --file /conda-envs/f19f15c6c742ae3e49b0435d689406c1/environment.yaml && \
     mamba env create --prefix /conda-envs/df2a53a81d11717a831dda8590f53cd5 --file /conda-envs/df2a53a81d11717a831dda8590f53cd5/environment.yaml && \
     mamba env create --prefix /conda-envs/7d12a67dde56d160f55937194337f2c4 --file /conda-envs/7d12a67dde56d160f55937194337f2c4/environment.yaml && \
     mamba env create --prefix /conda-envs/31753de779143be0587a030432205123 --file /conda-envs/31753de779143be0587a030432205123/environment.yaml && \

comparem2

@@ -19,7 +19,7 @@ __version__ = "2.14.1"
 # Conda
 # export COMPAREM2_BASE="$(realpath ~/comparem2)"; export COMPAREM2_PROFILE="${COMPAREM2_BASE}/profile/conda/default"; ${COMPAREM2_BASE}/comparem2 --config input_genomes="${COMPAREM2_BASE}/tests/E._faecium/*.fna" --until fast
 
-# If you haven't made any changes to the environment yamls, you can test using the apptainer/docker image.
+# If you haven't made any changes to the environment yamls, and there are no new versions of bundled software, you can test using the apptainer/docker image.
 # Apptainer
 # export COMPAREM2_BASE="$(realpath ~/comparem2)"; export COMPAREM2_PROFILE="${COMPAREM2_BASE}/profile/apptainer/default"; ${COMPAREM2_BASE}/comparem2 --config input_genomes="${COMPAREM2_BASE}/tests/E._faecium/*.fna" --until fast
 
@@ -28,8 +28,8 @@ __version__ = "2.14.1"
 # Update Dockerfile:
 # touch dummy1.fa dummy2.fa dummy3.fa; ./comparem2 --containerize | grep -A 10000 "FROM condaforge" | grep -B 10000 "mamba clean --all -y" > Dockerfile
 # And check that there is no  preceding or following text (comparem2 logo, status summary etc.).
-# The docker image can then be built: (example)
-# sudo docker build -t cmkobel/comparem2:v2.13 . && sudo docker push cmkobel/comparem2:v2.13
+# The docker image can then be built: (example only, remember to bump versions)
+# sudo docker build -t cmkobel/comparem2:v2.7 . && sudo docker push cmkobel/comparem2:v2.7
 
 # In case the exact same docker image should be used for consecutive versions of comparem2, although this shouldn't be the case when using the minor version for apptainer images only: (example)
 # sudo docker pull cmkobel/comparem2:v2.9