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Merge pull request #76 from singularityhub/update/containers-2022-12-01
[bot] update/containers-2022-12-01
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| url: https://biocontainers.pro/tools/circrna_finder | ||
| maintainer: '@vsoch' | ||
| description: singularity registry hpc automated addition for circrna_finder | ||
| latest: | ||
| 1.2--pl5321hdfd78af_0: sha256:caee621721cd157a319d54fa2af54a878f3cab9dc43eed69603cd2b0fb8f44ae | ||
| tags: | ||
| 1.2--pl5321hdfd78af_0: sha256:caee621721cd157a319d54fa2af54a878f3cab9dc43eed69603cd2b0fb8f44ae | ||
| docker: quay.io/biocontainers/circrna_finder | ||
| aliases: | ||
| filterCirc.awk: /usr/local/bin/filterCirc.awk | ||
| filterSpliceSiteCircles.pl: /usr/local/bin/filterSpliceSiteCircles.pl | ||
| nrForwardSplicedReads.pl: /usr/local/bin/nrForwardSplicedReads.pl | ||
| postProcessStarAlignment.pl: /usr/local/bin/postProcessStarAlignment.pl | ||
| runStar.pl: /usr/local/bin/runStar.pl | ||
| starCirclesToBed.pl: /usr/local/bin/starCirclesToBed.pl | ||
| basenc: /usr/local/bin/basenc | ||
| b2sum: /usr/local/bin/b2sum | ||
| base32: /usr/local/bin/base32 | ||
| base64: /usr/local/bin/base64 | ||
| basename: /usr/local/bin/basename | ||
| cat: /usr/local/bin/cat | ||
| chcon: /usr/local/bin/chcon | ||
| chgrp: /usr/local/bin/chgrp | ||
| chmod: /usr/local/bin/chmod | ||
| chown: /usr/local/bin/chown | ||
| chroot: /usr/local/bin/chroot | ||
| cksum: /usr/local/bin/cksum | ||
| comm: /usr/local/bin/comm | ||
| cp: /usr/local/bin/cp | ||
| csplit: /usr/local/bin/csplit | ||
| cut: /usr/local/bin/cut | ||
| date: /usr/local/bin/date | ||
| dd: /usr/local/bin/dd | ||
| df: /usr/local/bin/df | ||
| dir: /usr/local/bin/dir | ||
| dircolors: /usr/local/bin/dircolors | ||
| dirname: /usr/local/bin/dirname | ||
| du: /usr/local/bin/du | ||
| echo: /usr/local/bin/echo | ||
| env: /usr/local/bin/env |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| url: https://biocontainers.pro/tools/circtools | ||
| maintainer: '@vsoch' | ||
| description: singularity registry hpc automated addition for circtools | ||
| latest: | ||
| 1.2.1--pyh7cba7a3_0: sha256:7317627874031c4c9924d40b76602662a2d400c9ee4c1c626998c287e5e7bd65 | ||
| tags: | ||
| 1.2.1--pyh7cba7a3_0: sha256:7317627874031c4c9924d40b76602662a2d400c9ee4c1c626998c287e5e7bd65 | ||
| docker: quay.io/biocontainers/circtools | ||
| aliases: | ||
| DCC: /usr/local/bin/DCC | ||
| FUCHS: /usr/local/bin/FUCHS | ||
| circtools: /usr/local/bin/circtools | ||
| circtools_circtest_wrapper.R: /usr/local/bin/circtools_circtest_wrapper.R | ||
| circtools_detect_write_skip_tracks.pl: /usr/local/bin/circtools_detect_write_skip_tracks.pl | ||
| circtools_enrich_visualization.R: /usr/local/bin/circtools_enrich_visualization.R | ||
| circtools_exon_wrapper.R: /usr/local/bin/circtools_exon_wrapper.R | ||
| circtools_generate_flanking_introns.py: /usr/local/bin/circtools_generate_flanking_introns.py | ||
| circtools_generate_intron_gtf.sh: /usr/local/bin/circtools_generate_intron_gtf.sh | ||
| circtools_merge_enrich_results.sh: /usr/local/bin/circtools_merge_enrich_results.sh | ||
| circtools_primex_formatter.R: /usr/local/bin/circtools_primex_formatter.R | ||
| circtools_primex_wrapper.R: /usr/local/bin/circtools_primex_wrapper.R | ||
| circtools_quickcheck_wrapper.R: /usr/local/bin/circtools_quickcheck_wrapper.R | ||
| circtools_reconstruct_visualization.R: /usr/local/bin/circtools_reconstruct_visualization.R | ||
| circtools_sirna_formatter.R: /usr/local/bin/circtools_sirna_formatter.R | ||
| create_igv_script.py: /usr/local/bin/create_igv_script.py | ||
| create_igv_script_from_gene_names.py: /usr/local/bin/create_igv_script_from_gene_names.py | ||
| create_igv_script_from_position_list.py: /usr/local/bin/create_igv_script_from_position_list.py | ||
| detect_new_exons_from_fuchs_data.py: /usr/local/bin/detect_new_exons_from_fuchs_data.py | ||
| get_introns_from_ensembl.pl: /usr/local/bin/get_introns_from_ensembl.pl | ||
| guided_denovo_circle_structure_parallel: /usr/local/bin/guided_denovo_circle_structure_parallel | ||
| htseq-count-barcodes: /usr/local/bin/htseq-count-barcodes | ||
| make_coverage_picture.R: /usr/local/bin/make_coverage_picture.R | ||
| summarized_coverage_profiles.R: /usr/local/bin/summarized_coverage_profiles.R | ||
| htseq-count: /usr/local/bin/htseq-count | ||
| htseq-qa: /usr/local/bin/htseq-qa | ||
| fonttools: /usr/local/bin/fonttools | ||
| pyftmerge: /usr/local/bin/pyftmerge | ||
| pyftsubset: /usr/local/bin/pyftsubset | ||
| ttx: /usr/local/bin/ttx | ||
| brotli: /usr/local/bin/brotli | ||
| shiftBed: /usr/local/bin/shiftBed | ||
| annotateBed: /usr/local/bin/annotateBed | ||
| bamToBed: /usr/local/bin/bamToBed | ||
| bamToFastq: /usr/local/bin/bamToFastq | ||
| bed12ToBed6: /usr/local/bin/bed12ToBed6 | ||
| bedToBam: /usr/local/bin/bedToBam | ||
| bedToIgv: /usr/local/bin/bedToIgv | ||
| bedpeToBam: /usr/local/bin/bedpeToBam | ||
| bedtools: /usr/local/bin/bedtools | ||
| closestBed: /usr/local/bin/closestBed | ||
| clusterBed: /usr/local/bin/clusterBed | ||
| complementBed: /usr/local/bin/complementBed | ||
| coverageBed: /usr/local/bin/coverageBed | ||
| expandCols: /usr/local/bin/expandCols | ||
| fastaFromBed: /usr/local/bin/fastaFromBed | ||
| flankBed: /usr/local/bin/flankBed | ||
| genomeCoverageBed: /usr/local/bin/genomeCoverageBed | ||
| getOverlap: /usr/local/bin/getOverlap |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| url: https://biocontainers.pro/tools/ciriquant | ||
| maintainer: '@vsoch' | ||
| description: singularity registry hpc automated addition for ciriquant | ||
| latest: | ||
| 1.1.2--pyhdfd78af_1: sha256:bb17f17a4097078822ae961780fe332dd4f96c101459c8acd3bc207bb034f9c0 | ||
| tags: | ||
| 1.1.2--pyhdfd78af_1: sha256:bb17f17a4097078822ae961780fe332dd4f96c101459c8acd3bc207bb034f9c0 | ||
| docker: quay.io/biocontainers/ciriquant | ||
| aliases: | ||
| CIRI_DE: /usr/local/bin/CIRI_DE | ||
| CIRI_DE_replicate: /usr/local/bin/CIRI_DE_replicate | ||
| CIRIquant: /usr/local/bin/CIRIquant | ||
| compare_HLA.py: /usr/local/bin/compare_HLA.py | ||
| compare_HLA_Omixon.py: /usr/local/bin/compare_HLA_Omixon.py | ||
| extract_Omixon_HLA.py: /usr/local/bin/extract_Omixon_HLA.py | ||
| extract_exons.py: /usr/local/bin/extract_exons.py | ||
| extract_splice_sites.py: /usr/local/bin/extract_splice_sites.py | ||
| hisat2: /usr/local/bin/hisat2 | ||
| hisat2-align-l: /usr/local/bin/hisat2-align-l | ||
| hisat2-align-s: /usr/local/bin/hisat2-align-s | ||
| hisat2-build: /usr/local/bin/hisat2-build | ||
| hisat2-build-l: /usr/local/bin/hisat2-build-l | ||
| hisat2-build-s: /usr/local/bin/hisat2-build-s | ||
| hisat2-inspect: /usr/local/bin/hisat2-inspect | ||
| hisat2-inspect-l: /usr/local/bin/hisat2-inspect-l | ||
| hisat2-inspect-s: /usr/local/bin/hisat2-inspect-s | ||
| hisat2_extract_exons.py: /usr/local/bin/hisat2_extract_exons.py | ||
| hisat2_extract_snps_haplotypes_UCSC.py: /usr/local/bin/hisat2_extract_snps_haplotypes_UCSC.py | ||
| hisat2_extract_snps_haplotypes_VCF.py: /usr/local/bin/hisat2_extract_snps_haplotypes_VCF.py | ||
| hisat2_extract_splice_sites.py: /usr/local/bin/hisat2_extract_splice_sites.py | ||
| hisat2_read_statistics.py: /usr/local/bin/hisat2_read_statistics.py | ||
| hisat2_simulate_reads.py: /usr/local/bin/hisat2_simulate_reads.py | ||
| hisatgenotype.py: /usr/local/bin/hisatgenotype.py | ||
| hisatgenotype_HLA_genotyping_PGs.py: /usr/local/bin/hisatgenotype_HLA_genotyping_PGs.py | ||
| hisatgenotype_build_genome.py: /usr/local/bin/hisatgenotype_build_genome.py | ||
| hisatgenotype_convert_codis.py: /usr/local/bin/hisatgenotype_convert_codis.py | ||
| hisatgenotype_extract_codis_data.py: /usr/local/bin/hisatgenotype_extract_codis_data.py | ||
| hisatgenotype_extract_cyp_data.py: /usr/local/bin/hisatgenotype_extract_cyp_data.py | ||
| hisatgenotype_extract_reads.py: /usr/local/bin/hisatgenotype_extract_reads.py | ||
| hisatgenotype_extract_vars.py: /usr/local/bin/hisatgenotype_extract_vars.py | ||
| hisatgenotype_hla_cyp.py: /usr/local/bin/hisatgenotype_hla_cyp.py | ||
| hisatgenotype_locus.py: /usr/local/bin/hisatgenotype_locus.py | ||
| hisatgenotype_locus_samples.py: /usr/local/bin/hisatgenotype_locus_samples.py | ||
| prepDE.py: /usr/local/bin/prepDE.py | ||
| prep_CIRIquant: /usr/local/bin/prep_CIRIquant | ||
| run_extract_CP.sh: /usr/local/bin/run_extract_CP.sh | ||
| run_extract_ILMN.sh: /usr/local/bin/run_extract_ILMN.sh | ||
| run_genotype_build.sh: /usr/local/bin/run_genotype_build.sh | ||
| run_hisat2_build.sh: /usr/local/bin/run_hisat2_build.sh | ||
| run_type_CP.sh: /usr/local/bin/run_type_CP.sh | ||
| stringtie: /usr/local/bin/stringtie | ||
| qualfa2fq.pl: /usr/local/bin/qualfa2fq.pl | ||
| xa2multi.pl: /usr/local/bin/xa2multi.pl | ||
| bwa: /usr/local/bin/bwa | ||
| f2py2: /usr/local/bin/f2py2 | ||
| f2py2.7: /usr/local/bin/f2py2.7 | ||
| python2-config: /usr/local/bin/python2-config | ||
| python2.7-config: /usr/local/bin/python2.7-config | ||
| python2: /usr/local/bin/python2 | ||
| python2.7: /usr/local/bin/python2.7 | ||
| idle: /usr/local/bin/idle | ||
| python-config: /usr/local/bin/python-config | ||
| smtpd.py: /usr/local/bin/smtpd.py | ||
| ace2sam: /usr/local/bin/ace2sam | ||
| blast2sam.pl: /usr/local/bin/blast2sam.pl | ||
| bowtie2sam.pl: /usr/local/bin/bowtie2sam.pl | ||
| export2sam.pl: /usr/local/bin/export2sam.pl | ||
| interpolate_sam.pl: /usr/local/bin/interpolate_sam.pl | ||
| maq2sam-long: /usr/local/bin/maq2sam-long | ||
| maq2sam-short: /usr/local/bin/maq2sam-short | ||
| md5fa: /usr/local/bin/md5fa | ||
| md5sum-lite: /usr/local/bin/md5sum-lite | ||
| plot-bamstats: /usr/local/bin/plot-bamstats | ||
| psl2sam.pl: /usr/local/bin/psl2sam.pl | ||
| sam2vcf.pl: /usr/local/bin/sam2vcf.pl | ||
| samtools.pl: /usr/local/bin/samtools.pl |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| url: https://biocontainers.pro/tools/find_circ | ||
| maintainer: '@vsoch' | ||
| description: singularity registry hpc automated addition for find_circ | ||
| latest: | ||
| 1.2--hdfd78af_0: sha256:0e46cf8c9e35df7bd9a662528382f3e228194d880c40bfd717d3c061ed87d500 | ||
| tags: | ||
| 1.2--hdfd78af_0: sha256:0e46cf8c9e35df7bd9a662528382f3e228194d880c40bfd717d3c061ed87d500 | ||
| docker: quay.io/biocontainers/find_circ | ||
| aliases: | ||
| cmp_bed.py: /usr/local/bin/cmp_bed.py | ||
| find_circ.py: /usr/local/bin/find_circ.py | ||
| maxlength.py: /usr/local/bin/maxlength.py | ||
| merge_bed.py: /usr/local/bin/merge_bed.py | ||
| unmapped2anchors.py: /usr/local/bin/unmapped2anchors.py | ||
| f2py2: /usr/local/bin/f2py2 | ||
| f2py2.7: /usr/local/bin/f2py2.7 | ||
| python2-config: /usr/local/bin/python2-config | ||
| python2.7-config: /usr/local/bin/python2.7-config | ||
| python2: /usr/local/bin/python2 | ||
| python2.7: /usr/local/bin/python2.7 | ||
| idle: /usr/local/bin/idle | ||
| python-config: /usr/local/bin/python-config | ||
| smtpd.py: /usr/local/bin/smtpd.py |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| url: https://biocontainers.pro/tools/targetscan | ||
| maintainer: '@vsoch' | ||
| description: singularity registry hpc automated addition for targetscan | ||
| latest: | ||
| 7.0--pl5321hdfd78af_0: sha256:766449d7116d75961221a8937ee2687a815992b1ea5d4bff008e98bf5f7e9ac4 | ||
| tags: | ||
| 7.0--pl5321hdfd78af_0: sha256:766449d7116d75961221a8937ee2687a815992b1ea5d4bff008e98bf5f7e9ac4 | ||
| docker: quay.io/biocontainers/targetscan | ||
| aliases: | ||
| targetscan_70.pl: /usr/local/bin/targetscan_70.pl | ||
| perl5.32.1: /usr/local/bin/perl5.32.1 | ||
| streamzip: /usr/local/bin/streamzip |