diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 5b9e9a453..b521e521f 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -1,9 +1,9 @@ #targets base_image image_build -bioblend=1.0.0,galaxyxml=0.4.14,git=2.38.1,planemo=0.75.3 -cooltools=0.5.1,ucsc-bedgraphtobigwig=377 -cooltools=0.5.4,ucsc-bedgraphtobigwig=377 -python=3.9,scipy=1.8.0,numpy=1.22.3,iced=0.5.10,bx-python=0.8.13,pysam=0.19.0 -python=3.9,pandas=1.3.0,seaborn=0.11.0 +bioblend=1.0.0,galaxyxml=0.4.14,git=2.38.1,planemo=0.75.3 +cooltools=0.5.1,ucsc-bedgraphtobigwig=377 +cooltools=0.5.4,ucsc-bedgraphtobigwig=377 +python=3.9,scipy=1.8.0,numpy=1.22.3,iced=0.5.10,bx-python=0.8.13,pysam=0.19.0 +python=3.9,pandas=1.3.0,seaborn=0.11.0 bwa=0.7.17,samtools=1.10,samblaster=0.1.24 bgruening/busybox-bash:0.1 1 bowtie=1.1.1,picard=2.23.3 bgruening/busybox-bash:0.1 0 bwa-mem2=2.0,bwakit=0.7.17.dev1,samtools=1.10 bgruening/busybox-bash:0.1 0 @@ -50,7 +50,7 @@ snpeff=4.1 bgruening/busybox-bash:0.1 0 pandas=0.24.2,scipy=1.3.0 bgruening/busybox-bash:0.1 0 deeptools=3.1.2,samtools=1.7 bgruening/busybox-bash:0.1 0 wget=1.20.1 bgruening/busybox-bash:0.1 0 -wget=1.21.4 +wget=1.21.4 gawk=5.0.1 bgruening/busybox-bash:0.1 0 pyiron=0.2.2 bgruening/busybox-bash:0.1 0 pyiron=0.2.2,lammps=2019.06.05 bgruening/busybox-bash:0.1 0 @@ -78,440 +78,440 @@ varscan=2.4.2,samtools=1.3.1,tabix=0.2.6,grep=2.14 bgruening/busybox-bash:0.1 0 bedtools=2.27.1,grep=2.14,gawk=5.0.1 bgruening/busybox-bash:0.1 0 bedtools=2.27.1,grep=2.14,gawk=5.0.1,click=7,python=3.7 bgruening/busybox-bash:0.1 0 bedtools=2.17.0--0,python=2.7.13 bgruening/busybox-bash:0.1 0 -bedtools=2.23.0,pandas=1.5.2 +bedtools=2.23.0,pandas=1.5.2 bioconductor-rtracklayer=1.42.1,bioconductor-biostrings=2.50.2,r-optparse=1.6.4 bgruening/busybox-bash:0.1 0 bioconductor-dropletutils=1.6.1,openblas=0.3.9,r-matrix=1.2,r-ggplot2=3.2.1,r-optparse=1.6.4,r-gridextra=2.3,bioconductor-delayedarray=0.12.0 bgruening/busybox-bash:0.1 0 scipy=1.4.1,pandas=1.0.1 bgruening/busybox-bash:0.1 0 scipy=1.4.1,pandas=1.0.1,file=5.37 bgruening/busybox-bash:0.1 0 bx-python=0.7.1,galaxy-ops=1.0.0 bgruening/busybox-bash:0.1 1 r-seurat=3.1.5,r-rmarkdown=2.2 bioconda/extended-base-image:latest 0 -biopython=1.76 -cutadapt=1.8,perl -singularity=3.5.3 -bioconductor-biocgenerics=0.30.0,bioconductor-summarizedexperiment=1.14.0,metaphlan2=2.9.21,python=3.7.3,pyyaml=5.1.2,r-argparse=2.0.1,r-base=3.6.1,r-basejump=0.11.18,r-bcbiobase=0.6.10,r-bcbiornaseq=0.3.28,r-brio=0.3.11,r-deseqanalysis=0.2.10,r-goalie=0.3.10,sambamba=0.7.0 +biopython=1.76 +cutadapt=1.8,perl +singularity=3.5.3 +bioconductor-biocgenerics=0.30.0,bioconductor-summarizedexperiment=1.14.0,metaphlan2=2.9.21,python=3.7.3,pyyaml=5.1.2,r-argparse=2.0.1,r-base=3.6.1,r-basejump=0.11.18,r-bcbiobase=0.6.10,r-bcbiornaseq=0.3.28,r-brio=0.3.11,r-deseqanalysis=0.2.10,r-goalie=0.3.10,sambamba=0.7.0 bedtools=2.29.0,bioconductor-biocparallel=1.18.0,bioconductor-deseq2=1.24.0,bioconductor-limma=3.40.2,bioconductor-rhdf5=2.28.0,bioconductor-rtracklayer=1.44.2,bioconductor-tximport=1.12.3,bx-python=0.8.4,fastqc=0.11.7,gatk4=4.1.3.0,gffread=0.11.4,kallisto=0.46.0,kraken2=2.0.8_beta,multiqc=1.7,ngmerge=0.3,numpy=1.17.2,openjdk=8.0.192=h14c3975_1003,pandas=0.25.1,picard=2.19.2,pysam=0.15.4,python=3.6.7,qualimap=2.2.2c,r-argparse=2.0.1,r-data.table=1.12.2,r-dplyr=0.8.3,r-magrittr=1.5,rna-seqc=2.3.4,r-readr=1.3.1,r-stringi=1.4.3,r-xlsx=0.6.1,salmon=1.1.0,sambamba=0.7.0,samtools=1.9,star=2.7.2b,tzcode,ucsc-gtftogenepred=377 bgruening/busybox-bash:0.1 1 -r-readr=1.3.1 -ambertools=20.4 +r-readr=1.3.1 +ambertools=20.4 picard=2.22.8--0,bwa=0.7.17 bgruening/busybox-bash:0.1 0 whatshap=1.0--py37h9a982cc_1,tabix=0.2.6--ha92aebf_0 bgruening/busybox-bash:0.1 0 r-gridextra=2.3,bioconductor-cardinal=2.6.0 bioconda/extended-base-image:latest 0 rsem=1.3.3,star=2.7.6a bgruening/busybox-bash:0.1 0 -perl-io-uncompress-gunzip=2.064,pigz=2.3.4 -bowtie2=2.4.1,samtools=1.9,pigz=2.3.4 -bedtools=2.29.0,pigz=2.3.4 -pandas=0.24.2,pigz=2.3.4 -star=2.7.5b,samtools=1.9,pigz=2.3.4 -umi_tools=1.0.1,samtools=1.1.0 -icount=2.0.0,bedtools=2.28.0,pigz=2.3.4 -r-base=4.0.2,seacr=1.3,bedtools=2.29.2 -r-base=4.0.2,seacr=1.3,bedtools=2.30.0 -nanopolish=0.13.2,samtools=1.10,minimap2=2.17 -r-base=4.0.3,r-optparse=1.6.6,r-ggplot2=3.3.2,r-rcolorbrewer=1.1_2,r-pheatmap=1.0.12,bioconductor-deseq2=1.28.0,bioconductor-biocparallel=1.22.0,bioconductor-tximport=1.16.0,bioconductor-complexheatmap=2.4.2 +perl-io-uncompress-gunzip=2.064,pigz=2.3.4 +bowtie2=2.4.1,samtools=1.9,pigz=2.3.4 +bedtools=2.29.0,pigz=2.3.4 +pandas=0.24.2,pigz=2.3.4 +star=2.7.5b,samtools=1.9,pigz=2.3.4 +umi_tools=1.0.1,samtools=1.1.0 +icount=2.0.0,bedtools=2.28.0,pigz=2.3.4 +r-base=4.0.2,seacr=1.3,bedtools=2.29.2 +r-base=4.0.2,seacr=1.3,bedtools=2.30.0 +nanopolish=0.13.2,samtools=1.10,minimap2=2.17 +r-base=4.0.3,r-optparse=1.6.6,r-ggplot2=3.3.2,r-rcolorbrewer=1.1_2,r-pheatmap=1.0.12,bioconductor-deseq2=1.28.0,bioconductor-biocparallel=1.22.0,bioconductor-tximport=1.16.0,bioconductor-complexheatmap=2.4.2 fates-emerald=2.0.1 bioconda/extended-base-image:latest 0 trimmomatic=0.38,coreutils=8.25 bgruening/busybox-bash:0.1 0 -python=3.7 -python=3.8 -python=3.9 -samtools=1.11,bowtie=1.3.0 -samtools=1.15.1,bowtie=1.3.0 -samtools=1.16.1,bowtie=1.3.0 +python=3.7 +python=3.8 +python=3.9 +samtools=1.11,bowtie=1.3.0 +samtools=1.15.1,bowtie=1.3.0 +samtools=1.16.1,bowtie=1.3.0 searchgui=4.0.4,zip=3.0 bioconda/extended-base-image:latest 0 -bowtie2=2.4.2,samtools=1.11,pigz=2.3.4 +bowtie2=2.4.2,samtools=1.11,pigz=2.3.4 r-base=4.0,bioconductor-edger=3.32.0,bioconductor-limma=3.46.0,r-rjson=0.2.20,r-getopt=1.20.3,r-statmod=1.4.35,r-scales=1.1.1 bgruening/busybox-bash:0.1 0 qcat=1.1.0,pigz=2.3.4 bgruening/busybox-bash:0.1 0 -r-base=4.0.2,r-devtools=2.3.2,r-gmodels=2.18.1,r-optparse=1.6.6,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,bioconductor-genomicalignments=1.26.0,bioconductor-org.hs.eg.db=3.12.0,bioconductor-rsubread=2.4.0 -r-base=4.0.3,r-reshape2=1.4.4,r-optparse=1.6.6,r-ggplot2=3.3.3,r-scales=1.1.1,r-viridis=0.5.1,r-tidyverse=1.3.0,bioconductor-biostrings=2.58.0,bioconductor-complexheatmap=2.6.2 -metabat2=2.15,python=3.6.7,biopython=1.74,pandas=1.1.5 -cd-hit=4.8.1,exonerate=2.4,blast=2.11.0 -trinity=2.9.1,pigz=2.3.4 -biopython=1.78,pandas=1.1.2,numpy=1.18.1 -r-reshape2=1.4.4,r-plotly=4.9.2.1,plotly-orca=3.4.2,r-ggplot2=3.3.0,r-svglite=1.2.3,r-ggthemes=4.2.0,r-knitr=1.29,r-rmarkdown=2.3,r-kableextra=1.1.0 -velvet=1.2.10,oases=0.2.09 -pandas=1.1.5 -fred2=2.0.6,mhcflurry=1.4.3,mhcnuggets=2.3.2 -changeo=1.0.2,igblast=1.15.0 -homer=4.11,samtools=1.11,r-base=4.0.2,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,perl=5.26.2 -umi_tools=1.1.1,samtools=1.10 -pigz=2.3.4 -jq=1.6 -openjdk=8.0.121,python=2.7 -r-base=4.0.3,r-shazam=1.0.2,r-tigger=1.0.0 -r-base=4.0.3,r-shazam=1.0.2,r-tigger=1.0.0,tzdata=2021a -wget=1.20.1,biopython=1.78,igblast=1.15.0 +r-base=4.0.2,r-devtools=2.3.2,r-gmodels=2.18.1,r-optparse=1.6.6,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,bioconductor-genomicalignments=1.26.0,bioconductor-org.hs.eg.db=3.12.0,bioconductor-rsubread=2.4.0 +r-base=4.0.3,r-reshape2=1.4.4,r-optparse=1.6.6,r-ggplot2=3.3.3,r-scales=1.1.1,r-viridis=0.5.1,r-tidyverse=1.3.0,bioconductor-biostrings=2.58.0,bioconductor-complexheatmap=2.6.2 +metabat2=2.15,python=3.6.7,biopython=1.74,pandas=1.1.5 +cd-hit=4.8.1,exonerate=2.4,blast=2.11.0 +trinity=2.9.1,pigz=2.3.4 +biopython=1.78,pandas=1.1.2,numpy=1.18.1 +r-reshape2=1.4.4,r-plotly=4.9.2.1,plotly-orca=3.4.2,r-ggplot2=3.3.0,r-svglite=1.2.3,r-ggthemes=4.2.0,r-knitr=1.29,r-rmarkdown=2.3,r-kableextra=1.1.0 +velvet=1.2.10,oases=0.2.09 +pandas=1.1.5 +fred2=2.0.6,mhcflurry=1.4.3,mhcnuggets=2.3.2 +changeo=1.0.2,igblast=1.15.0 +homer=4.11,samtools=1.11,r-base=4.0.2,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,perl=5.26.2 +umi_tools=1.1.1,samtools=1.10 +pigz=2.3.4 +jq=1.6 +openjdk=8.0.121,python=2.7 +r-base=4.0.3,r-shazam=1.0.2,r-tigger=1.0.0 +r-base=4.0.3,r-shazam=1.0.2,r-tigger=1.0.0,tzdata=2021a +wget=1.20.1,biopython=1.78,igblast=1.15.0 cat=4.6,diamond=2.0.6 quay.io/bioconda/base-glibc-busybox-bash:2.1.0 1 -changeo=1.0.2,r-base=4.0.3,r-alakazam=1.0.2,igphyml=1.1.3 -changeo=1.0.2,r-base=4.0.3,r-alakazam=1.0.2,phylip=3.697 -r-base=4.0.3,r-alakazam=1.0.2,r-shazam=1.0.2 -yara=1.0.2,samtools=1.12 -yara=1.0.2,samtools=1.15.1 -yara=1.0.2,samtools=1.16.1 -pysam=0.16.0.1,biopython=1.78 -rapidnj=2.3.2,biopython=1.78 -r-base=4.1.1,r-optparse=1.7.1,r-argparse=2.1.3,bioconductor-genomicfeatures=1.46.1,bioconductor-grohmm=1.28.0 -kraken2=2.1.1,pigz=2.6 -merqury=1.1,tar=1.34,findutils=4.6.0 -star=2.6.1d,samtools=1.10 -star=2.6.1d,samtools=1.10,gawk=5.1.0 -planemo=0.74.3,git=2.30.2,galaxyxml=0.4.14 -minimap2=2.18,samtools=1.12 -changeo=1.0.2,igblast=1.15.0,wget=1.20.1 +changeo=1.0.2,r-base=4.0.3,r-alakazam=1.0.2,igphyml=1.1.3 +changeo=1.0.2,r-base=4.0.3,r-alakazam=1.0.2,phylip=3.697 +r-base=4.0.3,r-alakazam=1.0.2,r-shazam=1.0.2 +yara=1.0.2,samtools=1.12 +yara=1.0.2,samtools=1.15.1 +yara=1.0.2,samtools=1.16.1 +pysam=0.16.0.1,biopython=1.78 +rapidnj=2.3.2,biopython=1.78 +r-base=4.1.1,r-optparse=1.7.1,r-argparse=2.1.3,bioconductor-genomicfeatures=1.46.1,bioconductor-grohmm=1.28.0 +kraken2=2.1.1,pigz=2.6 +merqury=1.1,tar=1.34,findutils=4.6.0 +star=2.6.1d,samtools=1.10 +star=2.6.1d,samtools=1.10,gawk=5.1.0 +planemo=0.74.3,git=2.30.2,galaxyxml=0.4.14 +minimap2=2.18,samtools=1.12 +changeo=1.0.2,igblast=1.15.0,wget=1.20.1 changeo=1.3.0,igblast=1.22.0,wget=1.20.1 quay.io/bioconda/base-glibc-busybox-bash:2.1.0 1 -r-base=4.0.3,r-alakazam=1.0.2,r-shazam=1.0.2,r-kableextra=1.3.4,r-knitr=1.33,r-rmarkdown=2.8,r-stringr=1.4.0,r-dplyr=1.0.6 -bioconductor-biomart=2.46.3,bioconductor-deseq2=1.30.1,bioconductor-genomicranges=1.42.0,bioconductor-rtracklayer=1.50.0,bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2,r-base=4.0.3,r-dplyr=1.0.5,r-optparse=1.6.6,r-stringr=1.4.0,r-tidyr=1.1.3 -biopython=1.78,pigz=2.6 -python=3.9,pysam,biopython,click,pandas,numpy,ete3 -python=3.9,pigz=2.6,sed=4.8 -python=3.6,galaxy-ml=0.8.1 -python=3.6,galaxy-ml=0.7.12 -biopython=1.78,openpyxl=3.0.7,pyfastx=0.8.2,numpy=1.20.2,pandas=1.2.4 -python=3.9,biopython=1.78,openpyxl=3.0.7,pandas=1.2.4,rich=10.2.2,typer=0.3.2,xlsxwriter=1.4.3 -asciigenome=1.16.0,bedtools=2.30.0 +r-base=4.0.3,r-alakazam=1.0.2,r-shazam=1.0.2,r-kableextra=1.3.4,r-knitr=1.33,r-rmarkdown=2.8,r-stringr=1.4.0,r-dplyr=1.0.6 +bioconductor-biomart=2.46.3,bioconductor-deseq2=1.30.1,bioconductor-genomicranges=1.42.0,bioconductor-rtracklayer=1.50.0,bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2,r-base=4.0.3,r-dplyr=1.0.5,r-optparse=1.6.6,r-stringr=1.4.0,r-tidyr=1.1.3 +biopython=1.78,pigz=2.6 +python=3.9,pysam,biopython,click,pandas,numpy,ete3 +python=3.9,pigz=2.6,sed=4.8 +python=3.6,galaxy-ml=0.8.1 +python=3.6,galaxy-ml=0.7.12 +biopython=1.78,openpyxl=3.0.7,pyfastx=0.8.2,numpy=1.20.2,pandas=1.2.4 +python=3.9,biopython=1.78,openpyxl=3.0.7,pandas=1.2.4,rich=10.2.2,typer=0.3.2,xlsxwriter=1.4.3 +asciigenome=1.16.0,bedtools=2.30.0 r-recetox-aplcms=0.9.3,r-base=4.1.0,r-arrow=4.0.1 quay.io/bioconda/base-glibc-debian-bash:latest 0 -python=3.9,pandas=1.3.0,seaborn=0.11.0 +python=3.9,pandas=1.3.0,seaborn=0.11.0 bwa=0.7.17,samtools=1.9,bcftools=1.9 quay.io/bioconda/base-glibc-debian-bash:latest 0 retropath2_wrapper=2.4.0 quay.io/bioconda/base-glibc-debian-bash:latest 0 -star=2.7.9a,samtools=1.13,gawk=5.1.0 -star=2.7.9a,samtools=1.15.1,gawk=5.1.0 -star=2.7.9a,samtools=1.16.1,gawk=5.1.0 -python=3.9,pandas=1.3.0,seaborn=0.11.0,rich=10.6.0,typer=0.3.2,bcbio-gff=0.6.6,dna_features_viewer=3.0.3 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