diff --git a/CHANGELOG.md b/CHANGELOG.md index b773341e6..e95e4fd0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,10 +6,17 @@ This project adheres to [Semantic Versioning](http://semver.org/). ## [Develop] - HmtNote: annotate mitochondrial variants in VCF file +- Updating to latest and greatest versions ### Tools HmtNote: 0.7.2 +htslib: 1.10.2 -> 1.13 +cyrius v1.1 -> v1.1.1 +gatk 4.2.0.0 -> 4.2.2.0 +glnexus v1.3.1 -> v1.4.1 +multiqc 1.10.1 -> v1.11 +vep release_103.1 -> release_104.3 ### References diff --git a/containers/cyrius/Dockerfile b/containers/cyrius/Dockerfile index 2820e5102..ff7160c72 100644 --- a/containers/cyrius/Dockerfile +++ b/containers/cyrius/Dockerfile @@ -4,28 +4,28 @@ FROM clinicalgenomics/mip_base:2.1 ################## METADATA ###################### -LABEL base_image="clinicalgenomics/mip_base:2.1" -LABEL version="2" +LABEL base-image="clinicalgenomics/mip_base:2.1" +LABEL version="3" LABEL software="Cyrius" -LABEL software.version="v1.1" +LABEL software.version="v1.1.1" LABEL extra.binaries="star_caller.py" LABEL maintainer="Clinical-Genomics/MIP" WORKDIR /opt/conda/share ## Pysam errors when pip installing -RUN conda install pysam=0.16.0 && \ +RUN conda install pysam=0.16.0.1 && \ conda clean -ya ## Download and extract -RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.zip && \ - unzip v1.1.zip && \ - rm v1.1.zip +RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.1.zip && \ + unzip v1.1.1.zip && \ + rm v1.1.1.zip ## Move to directory and install requirements -RUN cd Cyrius-1.1 && \ - python -m pip install --no-cache-dir -r requirements.txt +RUN cd Cyrius-1.1.1 && \ + python -m pip install --no-cache-dir -r requirements.txt -RUN chmod a+x /opt/conda/share/Cyrius-1.1/star_caller.py +RUN chmod a+x /opt/conda/share/Cyrius-1.1.1/star_caller.py -ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1 +ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1.1 diff --git a/containers/htslib/Dockerfile b/containers/htslib/Dockerfile index ebf93e7a5..bc7081ada 100644 --- a/containers/htslib/Dockerfile +++ b/containers/htslib/Dockerfile @@ -1,17 +1,17 @@ ################## BASE IMAGE ###################### -FROM clinicalgenomics/mip_base:2.0 +FROM clinicalgenomics/mip_base:2.1 ################## METADATA ###################### -LABEL base_image="clinicalgenomics/mip_base:2.0" -LABEL version="5" +LABEL base-image="clinicalgenomics/mip_base:2.1" +LABEL version="6" LABEL software="htslib" -LABEL software.version="1.10.2" +LABEL software.version="1.13" LABEL extra.binaries="bcftools, bgzip, samtools, tabix" LABEL maintainer="Clinical-Genomics/MIP" -RUN conda install bcftools=1.10.2=hd2cd319_0 htslib=1.10.2=h78d89cc_0 samtools=1.10=h9402c20_2 +RUN conda install bcftools=1.13=h3a49de5_0 htslib=1.13=h9093b5e_0 samtools=1.13=h8c37831_0 ## Clean up after conda RUN /opt/conda/bin/conda clean -ya diff --git a/documentation/Setup.md b/documentation/Setup.md index b9ce86bf0..6ad7f04fd 100644 --- a/documentation/Setup.md +++ b/documentation/Setup.md @@ -45,19 +45,19 @@ You can speed up, for instance, the Readonly module by also installing the compa - [Chanjo] (version: 4.6.0) - [Chromograph] (version: 1.1) - [Cnvnator] (version: 0.4.1) -- [Cyrius] (version: v1.1) +- [Cyrius] (version: v1.1.1) - [Expansionhunter] (version 4.0.2) - [FastQC] (version: 0.11.9) - [Deepvariant] (version: 1.1.0) - [Delly] (version 0.8.7) -- [GATK] (version: 3.8.1 and 4.2.0.0) +- [GATK] (version: 3.8.1 and 4.2.2.0) - [GENMOD] (version: 3.7.3) - [Gffcompare] (version: 0.11.2) -- [Glnexus] (version: 1.3.1) -- [Htslib] (version: 1.10.2) +- [Glnexus] (version: v1.4.1) +- [Htslib] (version: 1.13) - [Manta] (version: 1.6.0) - [Megafusion] (version: 66a3a80) -- [MultiQC] (version: 1.10.1) +- [MultiQC] (version: v1.11) - [Pdfmerger] (version: 1.0) - [Peddy] (version: 0.4.3) - [PicardTools] (version: 2.25.0) @@ -81,7 +81,7 @@ You can speed up, for instance, the Readonly module by also installing the compa - [Varg] (version: 1.2.0) - [Vcf2cytosure] (version: 0.5.1) - [Vcfanno] (version: 0.3.2) -- [VEP] (version: 103.1) with plugin "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI" +- [VEP] (version: 104.3) with plugin "dbNSFP", "DisGeNET", "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI" The version number after the software name are tested for compatibility with MIP. diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml index 822bd9e3a..b7e8dffa4 100644 --- a/templates/mip_install_config.yaml +++ b/templates/mip_install_config.yaml @@ -52,7 +52,7 @@ container: cyrius: executable: star_caller.py: - uri: docker.io/clinicalgenomics/cyrius:v1.1 + uri: docker.io/clinicalgenomics/cyrius:v1.1.1 deepvariant: executable: run_deepvariant: /opt/deepvariant/bin/run_deepvariant @@ -85,7 +85,7 @@ container: gatk4: executable: gatk: - uri: docker.io/broadinstitute/gatk:4.2.0.0 + uri: docker.io/broadinstitute/gatk:4.2.2.0 genmod: executable: genmod: @@ -97,7 +97,7 @@ container: glnexus: executable: glnexus_cli: - uri: quay.io/mlin/glnexus:v1.3.1 + uri: ghcr.io/dnanexus-rnd/glnexus:v1.4.1 hmtnote: executable: hmtnote: @@ -108,7 +108,7 @@ container: bgzip: samtools: tabix: - uri: docker.io/clinicalgenomics/htslib:1.10.2 + uri: docker.io/clinicalgenomics/htslib:1.13 manta: executable: configManta.py: @@ -125,7 +125,7 @@ container: multiqc: executable: multiqc: - uri: docker.io/ewels/multiqc:1.10.1 + uri: docker.io/ewels/multiqc:v1.11 perl: executable: perl: @@ -248,9 +248,8 @@ container: vep: executable: vep: - uri: docker.io/ensemblorg/ensembl-vep:release_103.1 + uri: docker.io/ensemblorg/ensembl-vep:release_104.3 vcf2cytosure: executable: vcf2cytosure: uri: docker.io/jemten/vcf2cytosure:0.5.1 -