Skip to content

Commit

Permalink
forgot to upgrade two envs
Browse files Browse the repository at this point in the history
  • Loading branch information
Max Schubach committed Oct 9, 2024
1 parent bc54325 commit 81e5698
Show file tree
Hide file tree
Showing 3 changed files with 27 additions and 20 deletions.
43 changes: 25 additions & 18 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
ARG VERSION=0.1.1

FROM condaforge/mambaforge:latest
FROM condaforge/miniforge3:latest
LABEL io.github.snakemake.containerized="true"
LABEL io.github.snakemake.conda_env_hash="7a57714fe74eb25255d53b45e2095cd8a4dd4fe73db79006353670c432af97b1"

Expand Down Expand Up @@ -64,15 +64,15 @@ COPY workflow/envs/default.yaml /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8/env

# Conda environment:
# source: workflow/envs/fastqsplitter.yaml
# prefix: /conda-envs/3feb999aa5bcd4bbdbc57fef247c18cc
# prefix: /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f
# ---
# channels:
# - bioconda
# - conda-forge
# dependencies:
# - fastqsplitter
RUN mkdir -p /conda-envs/3feb999aa5bcd4bbdbc57fef247c18cc
COPY workflow/envs/fastqsplitter.yaml /conda-envs/3feb999aa5bcd4bbdbc57fef247c18cc/environment.yaml
RUN mkdir -p /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f
COPY workflow/envs/fastqsplitter.yaml /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f/environment.yaml

# Conda environment:
# source: workflow/envs/python3.yaml
Expand Down Expand Up @@ -112,7 +112,7 @@ COPY workflow/envs/r.yaml /conda-envs/ae3e37bf43cbb30416a885168e10c552/environme

# Conda environment:
# source: workflow/envs/python27.yaml
# prefix: /conda-envs/c2ee5a5886e2a786f23dd36e5c10752e
# prefix: /conda-envs/cb972f023533b03e742da9095ce03b06
# ---
# channels:
# - bioconda
Expand All @@ -122,8 +122,8 @@ COPY workflow/envs/r.yaml /conda-envs/ae3e37bf43cbb30416a885168e10c552/environme
# - pysam
# - python=2.7
# - samtools
RUN mkdir -p /conda-envs/c2ee5a5886e2a786f23dd36e5c10752e
COPY workflow/envs/python27.yaml /conda-envs/c2ee5a5886e2a786f23dd36e5c10752e/environment.yaml
RUN mkdir -p /conda-envs/cb972f023533b03e742da9095ce03b06
COPY workflow/envs/python27.yaml /conda-envs/cb972f023533b03e742da9095ce03b06/environment.yaml

# Conda environment:
# source: workflow/envs/cutadapt.yaml
Expand Down Expand Up @@ -158,17 +158,24 @@ COPY workflow/envs/quarto.yaml /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e/envi

# Step 2: Generate conda environments

RUN mamba env create --no-default-packages --prefix /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3 --file /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/f24b0ccfc23aadb93b466380cd592733 --file /conda-envs/f24b0ccfc23aadb93b466380cd592733/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1 --file /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8 --file /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/3feb999aa5bcd4bbdbc57fef247c18cc --file /conda-envs/3feb999aa5bcd4bbdbc57fef247c18cc/environment.yaml
RUN mamba env create --prefix /conda-envs/a4e1b935cbca52df9b6f192ff86c464c --file /conda-envs/a4e1b935cbca52df9b6f192ff86c464c/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/ae3e37bf43cbb30416a885168e10c552 --file /conda-envs/ae3e37bf43cbb30416a885168e10c552/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/c2ee5a5886e2a786f23dd36e5c10752e --file /conda-envs/c2ee5a5886e2a786f23dd36e5c10752e/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601 --file /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601/environment.yaml
RUN mamba env create --no-default-packages --prefix /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e --file /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e/environment.yaml
RUN <<EOR
conda config --add channels nodefaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
EOR

RUN conda env create --no-default-packages --prefix /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3 --file /conda-envs/8b5bbd33d7ccdbbe3a28773771abe2b3/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/f24b0ccfc23aadb93b466380cd592733 --file /conda-envs/f24b0ccfc23aadb93b466380cd592733/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1 --file /conda-envs/a0a27bbdca540d02023c7fdcf819bfc1/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601 --file /conda-envs/a3e2fce7f2f6fdbe1aa97232e3def601/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8 --file /conda-envs/899c0a8c04c6edeed4b242dbc3e0e1c8/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f --file /conda-envs/e5aec3a0d6b8921994e5305d4f89e90f/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/cb972f023533b03e742da9095ce03b06 --file /conda-envs/cb972f023533b03e742da9095ce03b06/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/a4e1b935cbca52df9b6f192ff86c464c --file /conda-envs/a4e1b935cbca52df9b6f192ff86c464c/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e --file /conda-envs/b933cc1aa7c25db04635e7ec0e37f80e/environment.yaml
RUN conda env create --no-default-packages --prefix /conda-envs/ae3e37bf43cbb30416a885168e10c552 --file /conda-envs/ae3e37bf43cbb30416a885168e10c552/environment.yaml

# cleanup when version changed
ARG VERSION
RUN mamba clean --all -y
RUN conda clean --all -y
2 changes: 1 addition & 1 deletion workflow/envs/fastqsplitter.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
---
channels:
- bioconda
- defaults
- conda-forge
dependencies:
- fastqsplitter
2 changes: 1 addition & 1 deletion workflow/envs/python27.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
channels:
- bioconda
- defaults
- conda-forge
dependencies:
- htslib
- pysam
Expand Down

0 comments on commit 81e5698

Please sign in to comment.