diff --git a/.github/workflows/docker-images.yml b/.github/workflows/docker-images.yml index 62aea63..0fdb79b 100644 --- a/.github/workflows/docker-images.yml +++ b/.github/workflows/docker-images.yml @@ -40,6 +40,7 @@ jobs: IFS="/" read -ra toolarr <<< "$changed_file" IFS="_" read -ra tagarr <<< "$changed_file" docker build --platform linux/amd64 -t ghcr.io/getwilds/${toolarr[0]}:${tagarr[-1]} -f ${changed_file} --push . + docker system prune -af sleep 5 fi done @@ -57,6 +58,7 @@ jobs: IFS="/" read -ra toolarr <<< "$changed_file" IFS="_" read -ra tagarr <<< "$changed_file" docker build --platform linux/amd64 -t getwilds/${toolarr[0]}:${tagarr[-1]} -f ${changed_file} --push . + docker system prune -af sleep 5 fi done diff --git a/annovar/Dockerfile_hg19 b/annovar/Dockerfile_hg19 index 4baaf82..e598292 100644 --- a/annovar/Dockerfile_hg19 +++ b/annovar/Dockerfile_hg19 @@ -32,3 +32,4 @@ RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene /annov # Cleanup RUN rm -rf annovar.latest.tar.gz + diff --git a/annovar/Dockerfile_hg38 b/annovar/Dockerfile_hg38 index 8a1db5b..c588e01 100644 --- a/annovar/Dockerfile_hg38 +++ b/annovar/Dockerfile_hg38 @@ -32,3 +32,4 @@ RUN annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene /annov # Cleanup RUN rm -rf annovar.latest.tar.gz /annovar/humandb/hg19_* + diff --git a/annovar/Dockerfile_latest b/annovar/Dockerfile_latest index 4e59929..3f8ca57 100644 --- a/annovar/Dockerfile_latest +++ b/annovar/Dockerfile_latest @@ -32,3 +32,4 @@ RUN annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene /annov # Cleanup RUN rm -rf annovar.latest.tar.gz + diff --git a/bcftools/Dockerfile_1.11 b/bcftools/Dockerfile_1.11 index 88e7b79..c7973fb 100644 --- a/bcftools/Dockerfile_1.11 +++ b/bcftools/Dockerfile_1.11 @@ -28,3 +28,4 @@ WORKDIR / ENV PATH="${PATH}:/bcftools-1.11" RUN rm -rf bcftools-1.11.tar.bz2 + diff --git a/bcftools/Dockerfile_1.19 b/bcftools/Dockerfile_1.19 index 82da78a..2c4f515 100644 --- a/bcftools/Dockerfile_1.19 +++ b/bcftools/Dockerfile_1.19 @@ -28,3 +28,4 @@ WORKDIR / ENV PATH="${PATH}:/bcftools-1.19" RUN rm -rf bcftools-1.19.tar.bz2 + diff --git a/bcftools/Dockerfile_latest b/bcftools/Dockerfile_latest index 1e4ed03..cf7e2fc 100644 --- a/bcftools/Dockerfile_latest +++ b/bcftools/Dockerfile_latest @@ -28,3 +28,4 @@ WORKDIR / ENV PATH="${PATH}:/bcftools-1.19" RUN rm -rf bcftools-1.19.tar.bz2 + diff --git a/biobambam2/Dockerfile_2.0.185 b/biobambam2/Dockerfile_2.0.185 index 6e0da6b..659207c 100644 --- a/biobambam2/Dockerfile_2.0.185 +++ b/biobambam2/Dockerfile_2.0.185 @@ -17,3 +17,4 @@ RUN apt-get update \ && apt-get install -y --no-install-recommends biobambam2=2.0.185+ds-1 \ && rm -rf /var/lib/apt/lists/* + diff --git a/biobambam2/Dockerfile_latest b/biobambam2/Dockerfile_latest index 9a41dc1..2d592f2 100644 --- a/biobambam2/Dockerfile_latest +++ b/biobambam2/Dockerfile_latest @@ -17,3 +17,4 @@ RUN apt-get update \ && apt-get install -y --no-install-recommends biobambam2=2.0.185+ds-1 \ && rm -rf /var/lib/apt/lists/* + diff --git a/picard/Dockerfile_3.1.1 b/picard/Dockerfile_3.1.1 index 027c183..64a6748 100644 --- a/picard/Dockerfile_3.1.1 +++ b/picard/Dockerfile_3.1.1 @@ -27,3 +27,4 @@ RUN export JAVA_HOME # Pulling Picard jar to a location that will persist in Apptainer RUN mkdir /usr/picard && wget -q --no-check-certificate -P /usr/picard/ \ https://github.com/broadinstitute/picard/releases/download/3.1.1/picard.jar + diff --git a/picard/Dockerfile_latest b/picard/Dockerfile_latest index a51114d..07a97d7 100644 --- a/picard/Dockerfile_latest +++ b/picard/Dockerfile_latest @@ -27,3 +27,4 @@ RUN export JAVA_HOME # Pulling Picard jar to a location that will persist in Apptainer RUN mkdir /usr/picard && wget -q --no-check-certificate -P /usr/picard/ \ https://github.com/broadinstitute/picard/releases/download/3.1.1/picard.jar + diff --git a/rnaseqc/Dockerfile_2.4.2 b/rnaseqc/Dockerfile_2.4.2 index c74050a..06f255f 100644 --- a/rnaseqc/Dockerfile_2.4.2 +++ b/rnaseqc/Dockerfile_2.4.2 @@ -31,3 +31,4 @@ WORKDIR /usr/rnaseqc RUN gunzip rnaseqc.v2.4.2.linux.gz && chmod a+x rnaseqc.v2.4.2.linux && mv rnaseqc.v2.4.2.linux rnaseqc WORKDIR / ENV PATH="${PATH}:/usr/rnaseqc" + diff --git a/rnaseqc/Dockerfile_latest b/rnaseqc/Dockerfile_latest index d2be3ef..0d887c8 100644 --- a/rnaseqc/Dockerfile_latest +++ b/rnaseqc/Dockerfile_latest @@ -31,3 +31,4 @@ WORKDIR /usr/rnaseqc RUN gunzip rnaseqc.v2.4.2.linux.gz && chmod a+x rnaseqc.v2.4.2.linux && mv rnaseqc.v2.4.2.linux rnaseqc WORKDIR / ENV PATH="${PATH}:/usr/rnaseqc" + diff --git a/samtools/Dockerfile_1.10 b/samtools/Dockerfile_1.10 index 1bbbb71..80de315 100644 --- a/samtools/Dockerfile_1.10 +++ b/samtools/Dockerfile_1.10 @@ -30,3 +30,4 @@ WORKDIR / # Cleanup RUN rm -rf samtools-1.10 samtools-1.10.tar.bz2 + diff --git a/samtools/Dockerfile_1.11 b/samtools/Dockerfile_1.11 index 42e4173..90b73a2 100644 --- a/samtools/Dockerfile_1.11 +++ b/samtools/Dockerfile_1.11 @@ -30,3 +30,4 @@ WORKDIR / # Cleanup RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2 + diff --git a/samtools/Dockerfile_latest b/samtools/Dockerfile_latest index d827743..471e108 100644 --- a/samtools/Dockerfile_latest +++ b/samtools/Dockerfile_latest @@ -30,3 +30,4 @@ WORKDIR / # Cleanup RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2 + diff --git a/scanpy/Dockerfile_1.10.2 b/scanpy/Dockerfile_1.10.2 index 7224f5e..f0b873f 100644 --- a/scanpy/Dockerfile_1.10.2 +++ b/scanpy/Dockerfile_1.10.2 @@ -14,3 +14,4 @@ LABEL org.opencontainers.image.licenses=MIT # Installing packages via pip RUN pip install --no-cache-dir scanpy==1.10.2 leiden-clustering==0.1.0 + diff --git a/scanpy/Dockerfile_latest b/scanpy/Dockerfile_latest index 7224f5e..f0b873f 100644 --- a/scanpy/Dockerfile_latest +++ b/scanpy/Dockerfile_latest @@ -14,3 +14,4 @@ LABEL org.opencontainers.image.licenses=MIT # Installing packages via pip RUN pip install --no-cache-dir scanpy==1.10.2 leiden-clustering==0.1.0 + diff --git a/scvi-tools/Dockerfile_1.1.6 b/scvi-tools/Dockerfile_1.1.6 index 6d8c195..be485e6 100644 --- a/scvi-tools/Dockerfile_1.1.6 +++ b/scvi-tools/Dockerfile_1.1.6 @@ -16,3 +16,4 @@ LABEL org.opencontainers.image.licenses=MIT # For GPU enabled abilities (from https://pytorch.org/get-started/locally/) - torch, torchvision, torchaudio RUN pip install --no-cache-dir scvi-tools==1.1.6 scanpy==1.10.2 leiden-clustering==0.1.0 scikit-misc==0.5.1 \ && pip install --no-cache-dir torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118 + diff --git a/scvi-tools/Dockerfile_latest b/scvi-tools/Dockerfile_latest index 6d8c195..be485e6 100644 --- a/scvi-tools/Dockerfile_latest +++ b/scvi-tools/Dockerfile_latest @@ -16,3 +16,4 @@ LABEL org.opencontainers.image.licenses=MIT # For GPU enabled abilities (from https://pytorch.org/get-started/locally/) - torch, torchvision, torchaudio RUN pip install --no-cache-dir scvi-tools==1.1.6 scanpy==1.10.2 leiden-clustering==0.1.0 scikit-misc==0.5.1 \ && pip install --no-cache-dir torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118 + diff --git a/umitools/Dockerfile_1.1.6 b/umitools/Dockerfile_1.1.6 index fefbed0..fecc1ae 100644 --- a/umitools/Dockerfile_1.1.6 +++ b/umitools/Dockerfile_1.1.6 @@ -14,3 +14,4 @@ LABEL org.opencontainers.image.licenses=MIT # Installing umi_tools via pip RUN pip install --no-cache-dir umi_tools==1.1.6 + diff --git a/umitools/Dockerfile_latest b/umitools/Dockerfile_latest index a19ed66..17f5aa0 100644 --- a/umitools/Dockerfile_latest +++ b/umitools/Dockerfile_latest @@ -14,3 +14,4 @@ LABEL org.opencontainers.image.licenses=MIT # Installing umi_tools via pip RUN pip install --no-cache-dir umi_tools==1.1.6 +