From b61647b4f8d390211fd8e6a15a9920ab4a6fa756 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 15:23:34 +0200 Subject: [PATCH 1/9] Rebuild the second batch --- combinations/hash.tsv | 50 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 8ad0cd073..68af8a3eb 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -660,3 +660,53 @@ cpt_gffparser=1.2.2,python=3.9,biopython=1.81 emboss=5.0.0,perl=5.26 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.6.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.7,coreutils=8.30 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +freebayes=1.0.2.29,gawk=4.1.3,samtools=0.1.19,parallel=20160622 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +seqtk=1.3,samtools=1.11,hisat2=2.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +seqtk=1.2,bzip2=1.0.6,salmon=0.11.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.11,bowtie2=2.4.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +r-rjson=0.2.20,r-getopt=1.20.2,bioconductor-dexseq=1.28.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +bx-python=0.7.1,ucsc-fatotwobit=324,six=1.10.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +biopython=1.70,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.12,winnowmap=2.03 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +anndata=0.7.5,loompy=2.0.17,scanpy=1.7.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +bcftools=1.10,matplotlib=3.1.0,htslib=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +gb_taxonomy_tools=1.0.0,gawk=4.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +python=3.9,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +screed=1.0.1,khmer=3.0.0a3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +csvtk=0.22.0,pangolin=2.3.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +r-gprofiler2=0.1.7,pandoc=2.7.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +bwameth=0.2.0,samtools=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +twobitreader=3.1.4,requests-cache=0.4.10,biopython=1.62 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +pigz=2.3.4,sra-tools=2.10.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +numpy=1.9,rpy2=2.8.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +pysam=0.15,matplotlib=3.1.2,cyvcf2=0.11.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +r-base=3.4.1,picard=2.18.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +scikit-image=0.14.2,pillow=5.3.0,scipy=1.2.1,tifffile=0.15.1,numpy=1.15.4 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +pigz=2.3.4,sra-tools=2.10.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +pretextsnapshot=0.0.3,rename=1.601 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +mageck=0.5.9.2,r-gplots=3.0.3,r-xtable=1.8_4,r-ggplot2=3.3.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +gawk=4.2.1,varscan=2.4.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +sra-tools=2.11.0,awscli=1.18.222,pigz=2.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +numpy=1.19.1,python=3.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +star=2.7.7a,samtools=1.9 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +tar=1.32,snippy=4.5.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +sed=4.7,fastqe=0.2.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +numpy=1.17,pandas=0.25 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +htslib=1.9,matplotlib=3.1.0,bcftools=1.9 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.9,bowtie2=2.3.4.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +bedtools=2.29.2,seacr=1.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +fates-emerald=2.0.1,python=3,binutils=2.35,perl-xml-libxml=2.0132,tar=1.32 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +sra-tools=2.10.3,samtools=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +r-base=3.4.1,rseqc=2.6.4 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +pysam=0.15,matplotlib=3.1.2,biopython=1.71 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +xarray=0.15.1,shapely=1.7.0,geopandas=0.7.0,python=3,netcdf4=1.5.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +cufflinks=2.2.1,bioconductor-cummerbund=2.16.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +sed=4.4,grep=2.14 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.10,pigz=2.5,awscli=1.18.222,sra-tools=2.10.9 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +samtools=1.6,bowtie2=2.3.4 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +mothur=1.39.5,vsearch=2.6.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +sailfish=0.10.1,bzip2=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +h5py=2.9.0,loompy=2.0.17,anndata=0.7.4 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From bd61ae83acb192b82f231179642bea1c57d87f7f Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 15:42:57 +0200 Subject: [PATCH 2/9] Fix attempt 1 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 68af8a3eb..5e28223e1 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -660,7 +660,6 @@ cpt_gffparser=1.2.2,python=3.9,biopython=1.81 emboss=5.0.0,perl=5.26 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.6.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.7,coreutils=8.30 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -freebayes=1.0.2.29,gawk=4.1.3,samtools=0.1.19,parallel=20160622 quay.io/bioconda/base-glibc-busybox-bash:latest 1 seqtk=1.3,samtools=1.11,hisat2=2.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 seqtk=1.2,bzip2=1.0.6,salmon=0.11.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.11,bowtie2=2.4.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From 0cd6fb31f426b63addcf75336e615e968db889d7 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 15:57:09 +0200 Subject: [PATCH 3/9] Fix attempt 2 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 5e28223e1..cc935156c 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -667,7 +667,6 @@ r-rjson=0.2.20,r-getopt=1.20.2,bioconductor-dexseq=1.28.1 quay.io/bioconda/base- bx-python=0.7.1,ucsc-fatotwobit=324,six=1.10.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 biopython=1.70,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.12,winnowmap=2.03 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -anndata=0.7.5,loompy=2.0.17,scanpy=1.7.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bcftools=1.10,matplotlib=3.1.0,htslib=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 gb_taxonomy_tools=1.0.0,gawk=4.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From 2c0b93da749c88150bf0c0b6e684b00011c2a663 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 16:18:06 +0200 Subject: [PATCH 4/9] Fix attempt 3 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index cc935156c..9c3e0b9cf 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -669,7 +669,6 @@ biopython=1.70,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.12,winnowmap=2.03 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bcftools=1.10,matplotlib=3.1.0,htslib=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -gb_taxonomy_tools=1.0.0,gawk=4.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.9,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 screed=1.0.1,khmer=3.0.0a3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From edba92a00e7743505a57da9b878c8d0e8042a66d Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 16:34:46 +0200 Subject: [PATCH 5/9] Fix attempt 4 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 9c3e0b9cf..a7b4591af 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -670,7 +670,6 @@ samtools=1.12,winnowmap=2.03 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bcftools=1.10,matplotlib=3.1.0,htslib=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.9,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -screed=1.0.1,khmer=3.0.0a3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 csvtk=0.22.0,pangolin=2.3.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From 6aba03506c611a0128817fcc0149a0477d4272c9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 16:58:39 +0200 Subject: [PATCH 6/9] Fix attempt 5 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index a7b4591af..e6a57d2a6 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -672,7 +672,6 @@ samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.9,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -csvtk=0.22.0,pangolin=2.3.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 r-gprofiler2=0.1.7,pandoc=2.7.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bwameth=0.2.0,samtools=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 twobitreader=3.1.4,requests-cache=0.4.10,biopython=1.62 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From b1a912ba6aa46d9d8dd3d9cc2ea9400f971102ae Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 17:27:05 +0200 Subject: [PATCH 7/9] Fix attempt 6 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index e6a57d2a6..8fed3a051 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -674,7 +674,6 @@ snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.i bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 r-gprofiler2=0.1.7,pandoc=2.7.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bwameth=0.2.0,samtools=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -twobitreader=3.1.4,requests-cache=0.4.10,biopython=1.62 quay.io/bioconda/base-glibc-busybox-bash:latest 1 pigz=2.3.4,sra-tools=2.10.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 numpy=1.9,rpy2=2.8.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 pysam=0.15,matplotlib=3.1.2,cyvcf2=0.11.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From 9482b1d623b85ecfdc326bd0918c855b1cb032f9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 17:54:55 +0200 Subject: [PATCH 8/9] Fix attempt 7 --- combinations/hash.tsv | 1 - 1 file changed, 1 deletion(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 8fed3a051..05c7eb9f1 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -674,7 +674,6 @@ snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.i bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 r-gprofiler2=0.1.7,pandoc=2.7.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 bwameth=0.2.0,samtools=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -pigz=2.3.4,sra-tools=2.10.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 numpy=1.9,rpy2=2.8.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 pysam=0.15,matplotlib=3.1.2,cyvcf2=0.11.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 r-base=3.4.1,picard=2.18.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 From f4aa8fd3cb09eb3fd8e129180b17a8a7bacee391 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Tue, 8 Jul 2025 18:32:52 +0200 Subject: [PATCH 9/9] Fix attempt 8 --- combinations/hash.tsv | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 05c7eb9f1..6124c7fbf 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -660,25 +660,6 @@ cpt_gffparser=1.2.2,python=3.9,biopython=1.81 emboss=5.0.0,perl=5.26 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.6.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 python=3.7,coreutils=8.30 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -seqtk=1.3,samtools=1.11,hisat2=2.1.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -seqtk=1.2,bzip2=1.0.6,salmon=0.11.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -samtools=1.11,bowtie2=2.4.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -r-rjson=0.2.20,r-getopt=1.20.2,bioconductor-dexseq=1.28.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -bx-python=0.7.1,ucsc-fatotwobit=324,six=1.10.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -biopython=1.70,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -samtools=1.12,winnowmap=2.03 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -bcftools=1.10,matplotlib=3.1.0,htslib=1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -samtools=1.9,sra-tools=2.9.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -python=3.9,tn93=1.0.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -snpeff=4.3.1t,biopython=1.70,libmagic=5.32,python-magic=0.4.15,python=3.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -bcbiogff=0.6.4,bedtools=2.27.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -r-gprofiler2=0.1.7,pandoc=2.7.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -bwameth=0.2.0,samtools=1.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -numpy=1.9,rpy2=2.8.5 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -pysam=0.15,matplotlib=3.1.2,cyvcf2=0.11.6 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -r-base=3.4.1,picard=2.18.2 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -scikit-image=0.14.2,pillow=5.3.0,scipy=1.2.1,tifffile=0.15.1,numpy=1.15.4 quay.io/bioconda/base-glibc-busybox-bash:latest 1 -pigz=2.3.4,sra-tools=2.10.8 quay.io/bioconda/base-glibc-busybox-bash:latest 1 pretextsnapshot=0.0.3,rename=1.601 quay.io/bioconda/base-glibc-busybox-bash:latest 1 mageck=0.5.9.2,r-gplots=3.0.3,r-xtable=1.8_4,r-ggplot2=3.3.0 quay.io/bioconda/base-glibc-busybox-bash:latest 1 gawk=4.2.1,varscan=2.4.3 quay.io/bioconda/base-glibc-busybox-bash:latest 1